So does this mean we will now have a "fork" of AmigaOS 68k at 3.1, so we'll have 3.9 which has to fall the way-side for official updates while 3.1 gets official updates?
Yeah, to me, it feels like 3.5/3.9 was a dead-end fork, and development has resumed based on 3.1. AmigaOS 4.1 is based on the 3.1 codebase as well, and AROS/MorphOS are made to be API-compatible with 3.1.
In terms of features and eye-candy out of the box, 3.9 is probably still the best, but what matters in the end is that all the tools, commands, libraries, patches etc.