diff --git a/src/Tasks/Microsoft.NET.Build.Tasks/RunReadyToRunCompiler.cs b/src/Tasks/Microsoft.NET.Build.Tasks/RunReadyToRunCompiler.cs
index e35ead24aece..e7a36b556429 100644
--- a/src/Tasks/Microsoft.NET.Build.Tasks/RunReadyToRunCompiler.cs
+++ b/src/Tasks/Microsoft.NET.Build.Tasks/RunReadyToRunCompiler.cs
@@ -23,7 +23,6 @@ public class RunReadyToRunCompiler : ToolTask
         public bool ShowCompilerWarnings { get; set; }
         public bool UseCrossgen2 { get; set; }
         public string Crossgen2ExtraCommandLineArgs { get; set; }
-        public string Crossgen2CompositeExtraCommandLineArgs { get; set; }
         public ITaskItem[] Crossgen2PgoFiles { get; set; }
         public string Crossgen2ContainerFormat { get; set; }
 
@@ -363,17 +362,6 @@ private string GenerateCrossgen2ResponseFile()
                 }
             }
 
-            // Arguments that are only valid for full composite builds (e.g. --strip-il-bodies).
-            // These arguments will not be applied to any assemblies that have been excluded from the composite image.
-            if (_createCompositeImage && !_partialCompile
-                && !string.IsNullOrEmpty(Crossgen2CompositeExtraCommandLineArgs))
-            {
-                foreach (string extraArg in Crossgen2CompositeExtraCommandLineArgs.Split([';'], StringSplitOptions.RemoveEmptyEntries))
-                {
-                    result.AppendLine(extraArg);
-                }
-            }
-
             if (_partialCompile)
             {
                 result.AppendLine("--partial");
diff --git a/src/Tasks/Microsoft.NET.Build.Tasks/targets/Microsoft.NET.CrossGen.targets b/src/Tasks/Microsoft.NET.Build.Tasks/targets/Microsoft.NET.CrossGen.targets
index a216e8010ea8..8e39f25b7cd1 100644
--- a/src/Tasks/Microsoft.NET.Build.Tasks/targets/Microsoft.NET.CrossGen.targets
+++ b/src/Tasks/Microsoft.NET.Build.Tasks/targets/Microsoft.NET.CrossGen.targets
@@ -46,12 +46,6 @@ Copyright (c) .NET Foundation. All rights reserved.
     <PublishReadyToRunCrossgen2ExtraArgs Condition="'$(PublishReadyToRunStripDebugInfo)' != 'false' and $(RuntimeIdentifier.StartsWith('iossimulator-'))">$(PublishReadyToRunCrossgen2ExtraArgs);--strip-debug-info</PublishReadyToRunCrossgen2ExtraArgs>
     <PublishReadyToRunCrossgen2ExtraArgs Condition="'$(PublishReadyToRunStripDebugInfo)' != 'false' and $(RuntimeIdentifier.StartsWith('tvossimulator-'))">$(PublishReadyToRunCrossgen2ExtraArgs);--strip-debug-info</PublishReadyToRunCrossgen2ExtraArgs>
     <PublishReadyToRunCrossgen2ExtraArgs Condition="'$(PublishReadyToRunStripDebugInfo)' != 'false' and $(RuntimeIdentifier.StartsWith('maccatalyst-'))">$(PublishReadyToRunCrossgen2ExtraArgs);--strip-debug-info</PublishReadyToRunCrossgen2ExtraArgs>
-
-    <PublishReadyToRunCrossgen2CompositeExtraArgs Condition="'$(PublishReadyToRunStripILBodies)' != 'false' and '$(PublishReadyToRunComposite)' == 'true' and '@(PublishReadyToRunPartialAssemblies)' == '' and '@(PublishReadyToRunCompositeExclusions)' == '' and $(RuntimeIdentifier.StartsWith('ios-'))">$(PublishReadyToRunCrossgen2CompositeExtraArgs);--strip-il-bodies</PublishReadyToRunCrossgen2CompositeExtraArgs>
-    <PublishReadyToRunCrossgen2CompositeExtraArgs Condition="'$(PublishReadyToRunStripILBodies)' != 'false' and '$(PublishReadyToRunComposite)' == 'true' and '@(PublishReadyToRunPartialAssemblies)' == '' and '@(PublishReadyToRunCompositeExclusions)' == '' and $(RuntimeIdentifier.StartsWith('tvos-'))">$(PublishReadyToRunCrossgen2CompositeExtraArgs);--strip-il-bodies</PublishReadyToRunCrossgen2CompositeExtraArgs>
-    <PublishReadyToRunCrossgen2CompositeExtraArgs Condition="'$(PublishReadyToRunStripILBodies)' != 'false' and '$(PublishReadyToRunComposite)' == 'true' and '@(PublishReadyToRunPartialAssemblies)' == '' and '@(PublishReadyToRunCompositeExclusions)' == '' and $(RuntimeIdentifier.StartsWith('iossimulator-'))">$(PublishReadyToRunCrossgen2CompositeExtraArgs);--strip-il-bodies</PublishReadyToRunCrossgen2CompositeExtraArgs>
-    <PublishReadyToRunCrossgen2CompositeExtraArgs Condition="'$(PublishReadyToRunStripILBodies)' != 'false' and '$(PublishReadyToRunComposite)' == 'true' and '@(PublishReadyToRunPartialAssemblies)' == '' and '@(PublishReadyToRunCompositeExclusions)' == '' and $(RuntimeIdentifier.StartsWith('tvossimulator-'))">$(PublishReadyToRunCrossgen2CompositeExtraArgs);--strip-il-bodies</PublishReadyToRunCrossgen2CompositeExtraArgs>
-    <PublishReadyToRunCrossgen2CompositeExtraArgs Condition="'$(PublishReadyToRunStripILBodies)' != 'false' and '$(PublishReadyToRunComposite)' == 'true' and '@(PublishReadyToRunPartialAssemblies)' == '' and '@(PublishReadyToRunCompositeExclusions)' == '' and $(RuntimeIdentifier.StartsWith('maccatalyst-'))">$(PublishReadyToRunCrossgen2CompositeExtraArgs);--strip-il-bodies</PublishReadyToRunCrossgen2CompositeExtraArgs>
   </PropertyGroup>
 
   <PropertyGroup>
@@ -511,7 +505,6 @@ Copyright (c) .NET Foundation. All rights reserved.
                            Crossgen2PgoFiles="@(_ReadyToRunPgoFiles)"
                            Crossgen2ContainerFormat="$(PublishReadyToRunContainerFormat)"
                            Crossgen2ExtraCommandLineArgs="$(PublishReadyToRunCrossgen2ExtraArgs)"
-                           Crossgen2CompositeExtraCommandLineArgs="$(PublishReadyToRunCrossgen2CompositeExtraArgs)"
                            ImplementationAssemblyReferences="@(_ReadyToRunAssembliesToReference)"
                            ShowCompilerWarnings="$(PublishReadyToRunShowWarnings)"
                            CompilationEntry="@(_ReadyToRunCompileList)"
diff --git a/test/Microsoft.NET.Build.Tests/GivenThatWeWantToBuildACppCliNonLibraryProject.cs b/test/Microsoft.NET.Build.Tests/GivenThatWeWantToBuildACppCliNonLibraryProject.cs
index a6c259b66678..1d746853b00e 100644
--- a/test/Microsoft.NET.Build.Tests/GivenThatWeWantToBuildACppCliNonLibraryProject.cs
+++ b/test/Microsoft.NET.Build.Tests/GivenThatWeWantToBuildACppCliNonLibraryProject.cs
@@ -13,7 +13,7 @@ public GivenThatWeWantToBuildACppCliNonLibraryProject(ITestOutputHelper log) : b
         {
         }
 
-        [FullMSBuildOnlyFact]
+        [FullMSBuildOnlyFact(Skip = "https://github.com/dotnet/sdk/issues/54145")]
         public void Given_an_exe_project_It_should_fail_with_error_message()
         {
             var testAsset = TestAssetsManager
@@ -27,7 +27,7 @@ public void Given_an_exe_project_It_should_fail_with_error_message()
                 .And.HaveStdOutContaining(Strings.NoSupportCppNonDynamicLibraryDotnetCore);
         }
 
-        [FullMSBuildOnlyFact]
+        [FullMSBuildOnlyFact(Skip = "https://github.com/dotnet/sdk/issues/54145")]
         public void Given_an_StaticLibrary_project_It_should_fail_with_error_message()
         {
             var testAsset = TestAssetsManager
diff --git a/test/dotnet.Tests/CommandTests/Run/RunFileTests_Directives.cs b/test/dotnet.Tests/CommandTests/Run/RunFileTests_Directives.cs
index 56db0c6c50e8..75f6a2e82d48 100644
--- a/test/dotnet.Tests/CommandTests/Run/RunFileTests_Directives.cs
+++ b/test/dotnet.Tests/CommandTests/Run/RunFileTests_Directives.cs
@@ -572,6 +572,7 @@ public static class Greeter
             }
             """);
 
+        // Duplicate #:ref directives are allowed (MSBuild can handle that).
         File.WriteAllText(filePath, """
             #:ref lib.cs
             #:ref lib.cs
@@ -581,8 +582,8 @@ public static class Greeter
         new DotnetCommand(Log, "run", relativeFilePath)
             .WithWorkingDirectory(testInstance.Path)
             .Execute()
-            .Should().Fail()
-            .And.HaveStdErrContaining(DirectiveError(filePath, 2, FileBasedProgramsResources.DuplicateDirective, "#:ref lib.cs"));
+            .Should().Pass()
+            .And.HaveStdOut("Hello!");
 
         File.WriteAllText(filePath, """
             #:ref lib.cs
@@ -590,7 +591,6 @@ public static class Greeter
             Console.WriteLine(MyLib.Greeter.Greet());
             """);
 
-        // https://github.com/dotnet/sdk/issues/51139: we should detect the duplicate ref
         new DotnetCommand(Log, "run", relativeFilePath)
             .WithWorkingDirectory(testInstance.Path)
             .Execute()
@@ -603,7 +603,6 @@ public static class Greeter
             Console.WriteLine(MyLib.Greeter.Greet());
             """);
 
-        // https://github.com/dotnet/sdk/issues/51139: we should detect the duplicate ref
         new DotnetCommand(Log, "run", relativeFilePath)
             .WithWorkingDirectory(testInstance.Path)
             .Execute()