Not sure about 3.1 but with 3.9 you are correct. There was quite a few individual contributors of some components and the rights passed back to them. There is a discussion on amiga.org about this and a couple of the contributors are on there.
As for 3.x, Cloanto has reworked some of it beyond what was in 3.9, some of the files are quite recent too. The same for the 3.1 ROM, Cloanto has released a new version with large disk support and other enhancements.
It is very much still alive.