These are however the same on Linux - mesa may change, but what the app uses is OpenGL and GLX. A more modern app might use EGL instead of GLX, or have switched to Vulkan, but that doesn't break old code.
You can also run an old mesa from the time the app was built if it supports your newer hardware, but I'd rather consider that to be part of the platform the same way you'd consider the DirectX libraries to be part of windows.
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.
You can also run an old mesa from the time the app was built if it supports your newer hardware, but I'd rather consider that to be part of the platform the same way you'd consider the DirectX libraries to be part of windows.