This use case is indeed not very well supported currently. The best option for now would be to link your repo to one SonarCloud project (for instance for the C# part), and to manually create another project in SonarCloud that is not bound to this repo so that you can run the analysis for the other part.
We plan to improve a lot the way we trigger analyses, especially to not heavily depend on the build system. This should allow us to support your configuration out of the box. However, I can’t give you any ETA - we just started discussing about this a couple of weeks ago.