There is now $configuration.CodeCoverage.UseBreakpoints experimental flag that allows you to use Profiler based code coverage instead of breakpoints based code coverage.
Here is a fuller example of generating CC for your code base using both methods.
https://gist.github.com/nohwnd/3a29c8f4afc21329a146b5cba953d503
If you can please try it and compare the xmls. E.g. open both in vscode and use the Compare active file with... command from the command pallete. You should see only difference on the top in timestamps.
This should work from PS3 up. At least it does in our CI pipeline.