So after doing some deep dives yesterday I think I narrowed the issue down to mesa:
There’s probably some drm/amd issues at play as well since a lot of new issues were opened there the past week about amd pageflips or ring gfx time-outs but perhaps they’re related:
There are some suggested fixes in the mesa issue like downgrading mesa versions but hopefully mesa will just get a hotfix release soon.
I used sudo downgrade mesa and switched to mesa 24.3.4 from 2025-01-23 and so far it seems that my artefacts are gone. Godot also seems to launch much smoother than with mesa 25.