Did not run into this problem specifically, but ran into others, which required modification to the csproj file in the godot build to match the project settings, and setting up local nuget store to use the proper matching package version. (Also requires rebuilding the templates.) The most interesting problem I ran into was that I had to set up the emscc build on WSL, because some commands are too long for windows powershell.
I think the project was originally godot 4.0.1, then upgraded to 4.4.1, then built wit the custom godot build... not sure if the contents of the .godot folder (which is not included in my repo) are relevant for your errors, but resource handling changed over time... I would try to import and build the project with previous version of godot before buiding with the custom one.