OK, so, status update:

The full patch I'm applying looks like this:

diff --git a/src/runtime/src/coreclr/tools/aot/ILCompiler/ILCompiler.csproj b/src/runtime/src/coreclr/tools/aot/ILCompiler/ILCompiler.csproj
index 7122c81034..924b1e7d45 100644
--- a/src/runtime/src/coreclr/tools/aot/ILCompiler/ILCompiler.csproj
+++ b/src/runtime/src/coreclr/tools/aot/ILCompiler/ILCompiler.csproj
@@ -11,7 +11,6 @@
   <PropertyGroup Condition="'$(BuildingInsideVisualStudio)' != 'true'">
     <PublishDir>$(RuntimeBinDir)ilc-published/</PublishDir>
     <!-- Can't use NativeAOT in source build yet https://github.com/dotnet/runtime/issues/66859 -->
-    <NativeAotSupported Condition="'$(DotNetBuildFromSource)' == 'true'">false</NativeAotSupported>
     <!-- Disable native AOT on FreeBSD when cross building from Linux. -->
     <NativeAotSupported Condition="'$(TargetOS)' == 'freebsd' and '$(CrossBuild)' == 'true'">false</NativeAotSupported>
     <PublishAot Condition="'$(NativeAotSupported)' == 'true'">true</PublishAot>
diff --git a/src/runtime/src/coreclr/tools/aot/crossgen2/crossgen2.csproj b/src/runtime/src/coreclr/tools/aot/crossgen2/crossgen2.csproj
index ef1b82f537..9789cefda2 100644
--- a/src/runtime/src/coreclr/tools/aot/crossgen2/crossgen2.csproj
+++ b/src/runtime/src/coreclr/tools/aot/crossgen2/crossgen2.csproj
@@ -5,11 +5,9 @@
   <PropertyGroup>
     <OutputPath>$(RuntimeBinDir)crossgen2</OutputPath>
     <!-- Can't use NativeAOT in source build yet https://github.com/dotnet/runtime/issues/66859 -->
-    <NativeAotSupported Condition="'$(DotNetBuildFromSource)' == 'true'">false</NativeAotSupported>
     <!-- Trimming is not currently working, but set the appropriate feature flags for NativeAOT -->
     <PublishTrimmed Condition="'$(NativeAotSupported)' == 'true'">true</PublishTrimmed>
-    <RuntimeIdentifiers Condition="'$(_IsPublishing)' != 'true' and '$(DotNetBuildFromSource)' != 'true'">linux-x64;linux-musl-x64;linux-arm;linux-musl-arm;linux-arm64;linux-musl-arm64;freebsd-x64;freebsd-arm64;osx-x64;osx-arm64;win-x64;win-x86;win-arm64</RuntimeIdentifiers>
-    <RuntimeIdentifiers Condition="'$(DotNetBuildFromSource)' == 'true'">$(PackageRID)</RuntimeIdentifiers>
+    <RuntimeIdentifiers Condition="'$(_IsPublishing)' != 'true'">linux-x64;linux-musl-x64;linux-arm;linux-musl-arm;linux-arm64;linux-musl-arm64;freebsd-x64;freebsd-arm64;osx-x64;osx-arm64;win-x64;win-x86;win-arm64</RuntimeIdentifiers>
     <SelfContained>false</SelfContained>
     <SelfContained Condition="'$(_IsPublishing)' == 'true'">true</SelfContained>
   </PropertyGroup>
diff --git a/src/runtime/eng/native/build-commons.sh b/src/runtime/eng/native/build-commons.sh
index d9eb04cd8a..3dcae0f254 100755
--- a/src/runtime/eng/native/build-commons.sh
+++ b/src/runtime/eng/native/build-commons.sh
@@ -514,6 +514,7 @@ while :; do
 
     shift
 done
+__PortableBuild=1
 
 if [[ -z "$__HostArch" ]]; then
     __HostArch=$__TargetArch
diff --git a/src/installer/src/redist/targets/GenerateLayout.targets b/src/installer/src/redist/targets/GenerateLayout.targets
index 9ce7496291..bfe353f1b0 100644
--- a/src/installer/src/redist/targets/GenerateLayout.targets
+++ b/src/installer/src/redist/targets/GenerateLayout.targets
@@ -38,7 +38,7 @@
 
       <CoreSetupRid Condition="'$(CoreSetupRid)' == ''">$(HostRid)</CoreSetupRid>
       <CoreSetupRid Condition=" ('$(OSName)' == 'win' or '$(OSName)' == 'osx' or '$(OSName)' == 'freebsd') and '$(DotNetBuildFromSource)' != 'true' ">$(OSName)-$(Architecture)</CoreSetupRid>
-      <CoreSetupRid Condition="$(HostRid.StartsWith('mariner.2.0'))">$(HostRid.Replace('mariner.2.0', 'cm.2'))</CoreSetupRid>
+      <!-- wtf <CoreSetupRid Condition="$(HostRid.StartsWith('mariner.2.0'))">$(HostRid.Replace('mariner.2.0', 'cm.2'))</CoreSetupRid>-->
 
       <!-- only the runtime OSX .pkgs have a `-internal` suffix -->
       <InstallerStartSuffix Condition="$([MSBuild]::IsOSPlatform('OSX'))">-internal</InstallerStartSuffix>
diff --git a/repo-projects/runtime.proj b/repo-projects/runtime.proj
index 67959e981d..cfe10b9dc7 100644
--- a/repo-projects/runtime.proj
+++ b/repo-projects/runtime.proj
@@ -22,10 +22,11 @@
     <BaseOS>$(NETCoreSdkPortableRuntimeIdentifier.Substring(0, $(_platformIndex)))</BaseOS>
 
     <BuildCommandArgs>$(StandardSourceBuildArgs)</BuildCommandArgs>
+    <BuildCommandArgs>$(BuildCommandArgs) --arch arm64</BuildCommandArgs>
     <BuildCommandArgs>$(BuildCommandArgs) /p:TargetRid=$(OverrideTargetRid)</BuildCommandArgs>
     <BuildCommandArgs>$(BuildCommandArgs) /p:RuntimeOS=$(RuntimeOS)</BuildCommandArgs>
     <BuildCommandArgs>$(BuildCommandArgs) /p:BaseOS=$(BaseOS)</BuildCommandArgs>
-    <BuildCommandArgs>$(BuildCommandArgs) /p:SourceBuildNonPortable=true</BuildCommandArgs>
+    <BuildCommandArgs>$(BuildCommandArgs) /p:SourceBuildNonPortable=false</BuildCommandArgs>
     <BuildCommandArgs>$(BuildCommandArgs) /p:UsingToolMicrosoftNetCompilers=false</BuildCommandArgs>
     <BuildCommand>$(StandardSourceBuildCommand) $(BuildCommandArgs)</BuildCommand>
   </PropertyGroup>

The csproj changes are needed for restore to work on runtime. --arch being hardcoded in runtime.proj is obviously wrong, but it needs adding somehow. The other changes are from one of my other issues.

I'm building with docker run -e CROSSCOMPILE=1 -e ROOTFS_DIR=/crossrootfs/arm64 -w pwd--platform linux/amd64 -vpwd:pwd -it mcr.microsoft.com/dotnet-buildtools/prereqs:cbl-mariner-2.0-cross-arm64 ./build.sh --online --use-mono-runtime -- /p:OverrideTargetRid=linux-arm64

There is obviously a bunch of architecture confusion still in the build:

artifacts in artifacts/x64/Release/
some of those artifacts have -x64 filename suffixes
Private.SourceBuilt.Prebuilts.8.0.100-rtm.23526.1.mariner.2.0-x64.tar.gz contains an x64 runtime pack, as well as arm64
Some files in artifacts/obj/x64/Release/blob-feed/assets/ have x64 suffix, especially symbols packages

Also, the build only works with Mono runtime, because one of the things the CoreCLR build tries to build is a component called crosscomponents, for x64 (build arch). We need to figure out what to do for this if we want CoreCLR to work.

But... it seems functional for a proof-of-concept. I also tested the patch above on Mac, and got an osx-arm64 build when using arch -x86_64 to force x64 host platform detection

[VMR] Add cross build support #3671

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