Ah apologies, you're right - I was tired and read things wrong.
But I suspect "GL issues" (i.e., GL API stability) is being mixed together with e.g. mesa issues if mesa is being bundled inside the app/in a "flatpak SDK" instead of being treated as a system library akin to what you would do with DirectX.
Mesa contains your graphics driver and window system integrations, so when the system changes so must mesa change - but the ABI exposed to clients does not change, other than new features being added.
An example from another comment: https://news.ycombinator.com/item?id=43519949