You can use mono for targets that need it and .NET 6 for those that don't
Keeping two implementations side by side would be expensive to maintain and not a good user experience: you start writing nice, "modern" .NET6 code and then need to rewrite things to run on top of .NET4-ish (and the older BCL and C#).
And I think .NET6 supports mobile now?
Mono was largely folded into CoreCLR a couple releases ago and part of that infrastructure is used to support some targets like mobile and WebAssembly.
[disclosure: I work on Mono at Microsoft.]
Yet Godot manages it, with a volunteer team and a better overall user experience.