I think the wise decision here would be to give up on generating lightmap UVs.
- The UV generation algorithm was “ok” 10 years ago. I think we can consider it bad now (and it has actually gotten worse with time).
- It still has cross-platform issues. Open the same project on a Mac (or a different brand CPU) and the UVs might generate a bit differently on import, making your Lightmaps invalid. (this was partially addressed by Alexey in the Unity 3-4.x days, but hasn’t been touched since AFAIK and it’s one of those things that need to be at 100% to not be an issue).
- If they start tweaking it, upgrading to a new Unity version will also invalidate your lightmaps. Unless of course they change how it works (and the generated UVs are stored somewhere so they don’t have to be generated if you aren’t baking new lightmaps), but I wouldn’t hold my breath.
- For whatever reason, the lightmapping team has had other priorities for many years. It took them a couple of years to fix serious regressions in the way the islands are packed (and they still haven’t fixed all of them…) (related link: Packing continues to be horrible, please fix )
At this point, I can’t imagine them addressing all the above in one fell swoop, and if they don’t address them all, then the feature is not reliable enough to be worth using. Make your own UVs. I use Rizom UV, it’s good.
Only use UV generation for throwaway UVs while you are still changing things a lot. Once your levels start stabilizing a bit, make UVs manually.