Anyway the thing is to wait for the Scintilla change to ripple through Scintilla LTS branch and into Geany and see if its better (and if other fonts are worse :(
This already happened, the change is in the Scintilla 3.20.0 release and it works on my system, i.e. I do see underscores again.
So, we just need to update Scintilla and get this resolved (at least for some or ideally most users). I'll give it a shot.