I think the problem is that you chose .NET 4.5.2 or similar (.net full) output, and that therefore uses the 'old' csproj format. The vsproject file generator will then look for the file in that format. As it's in a different format, it can't 'adjust' it and adds the nodes it needs. It's always overwritten, it just adds a lot of data you don't need.
If you select .net standard 2.0 as the output when generating code, you'll get the new format and it shouldn't overwrite the project file/augment it. The generated code is the same (it doesn't generate an assemblyinfo.cs file, but that's ok, the new project format doesn't need it).
We use that too for our generated test projects which all target multiple platforms (.net 4.5.2 and .netstandard20)