You might look into patching your Kobo. There are lots of patches dealing with formatting quirks (advanced font control, font sizes, margins, line height) for both epubs and kepubs. I've found them to be very useful.
Still, if all your custom fonts display as bold in your epubs, then there's something wrong with the font metadata. That can be fixed with FontForge. I dimly remember having the same issue with one of my fonts (I think it was Bookerly) when I first got my Libra. Changing the metadata for this font fixed that.
Edit: here are very useful instructions for fixing fonts:
https://wiki.mobileread.com/wiki/Kob...play_Correctly