I'm on KDE. It's quite an odd problem. If I keep them both set to refresh rates below their max, things work fine. However, if both monitors are set to their native refresh rates, the higher refresh rate one goes blank and the lower one starts flickering. If I disable the lower refresh rate monitor, I can set the higher one to it's max without issue though.
Essentially, when I'm booting into Bazzite, I need to either disable my second monitor or halve my refresh rate or it's unusable.