URP is using in-memory assets without saving them

Scopely migrated from Unity 6000.1.0f1 to 6000.1.17f1. The team is using Asset Bundles via the Legacy Build Pipeline, After migration  they started to see a drastic jump in build times; what used to take 20 minutes per incremental build per platform, jumped to 3 hours+ . The issue is introduced by [Internal link]
 
In a nutshell, the important bit of that small commit is in 

BuildAssetBundle.cpp

, where 2 calls to 

Scripting::UnityEditor::Build::BuildPipelineInterfacesProxy::InitializeBuildCallbacks(kAllAssetBundleProcessors);

 were moved to 

BuildAssetBundlesImplementation

Before, they were done early, inside our two flavours of 

BuildAssetBundles 

one that does it from the asset Database, and the one that does it from AssetBundleBuildInfos.
These two then called 

BuildAssetBundlesImplementation 

, which does the hefty lifting.
Now, the call to the InitializeBuildCallbacks is done properly, after the BuildTarget stuff is initialized. This is the intended fix.
Now, this causes an issue when you use URP. Because this call is now done AFTER BuildAssetBundlesImplementation calls AssetDatabase.SaveAssets(). This means that now, any asset changed inside the initialization of the callbacks (debatable if that should happen), is not saved to disc. Before, they were saved.
This is crucial for URP though, because of its UpdateShaderPrefilterDataBeforeBuild:
 

class UpdateShaderPrefilteringDataBeforeBuild : IPreprocessShaders {     public int callbackOrder => -100;       public UpdateShaderPrefilteringDataBeforeBuild()     {         ShaderBuildPreprocessor.GatherShaderFeatures(Debug.isDebugBuild);     }   public void OnProcessShader(Shader shader, ShaderSnippetData snippetData, IList<ShaderCompilerData> compilerDataList){} }

 
As you see, this IPreprocessShaders is not just initializing stuff, it's actually doing work in the constructor. And that work changes the URP Asset content in memory.
So before the fix, URP was doing its change as part of the process initialization code, then the build asset bundle implementation was saving them to disc. Now it's not.
This is crucial, because when building bundles that contain shaders, the hash of the bundle includes the hash of the URP Asset. If it was not saved, the bundle are going to use the old one.