Thanks for the project. We took a look and found some problems with how images are packed after the first page. We've improved this quite a bit in v4.2 and now your images pack into 3 pages again. They just barely fit in 3 pages.
In general it's not possible to rely on packing to take the same number of pages for newer Spine versions. This is because packing is NP hard, meaning it is not possible to calculate the absolute most efficient packing. Instead we must use heuristics to do the job in a "best effort" manner. Sometimes we need to make changes to the texture packer and this can cause images that were packed on, for example, 3 pages to be packed on 4 instead. This is not a bug, it just means when it fit on 3 pages you got lucky that the particular heuristics managed to make it fit.
The packer in 3.8 can take an extraordinary amount of time. When there are many images (say 1000+) it could take many hours or even days. The packer in 4.1+ is much improved and should complete a lot faster, but the changes to do that (and other things) may have changed the packing results slightly, possibly changing the number of pages in the unlucky case.
Thankfully in this particular case by us carefully looking into the texture packer due to your report, we found actual bugs and fixing them improved packing enough that you can still fit on 3 pages. Cheers! 🍻