Cloanto does not have rights on 3.9 or 3.5. They are entirely at H&P and at contributing parties, not at Cloanto. So while I certainly do not know how agreements with other parties were made back then, I hold rights on ViNCEd and BenchTrash all alike, also on the IOTools and probably a couple of other components I forgot. Me alone, and not Cloanto, and neither Hyperion, and neither H&P anymore, which just had a 2 years limited licence. I just decided that 3.1.4 was not the right place to include my contribution, so everybody is invited to get them from Aminet if found appropriate.
In fact, unless there is some hidden earlier agreement between Amiga Inc. and Cloanto that predates the settlement agreement beyond what I know, Cloanto could not have developped 3.X in first place (did they even develop anything?) without having development rights which were (negotiated) exclusively to be at Hyperion's side. As far as I know, Cloanto has sufficient rights "for emulation purposes", which does not state much. They can surely sell ROM images (1.2 up to 3.1 even), they may even have rights on the source code for 1.3, but none of that would have helped for 3.1.4 in any particular way.
3.1.4 with Cloanto would have been a much harder work, and it would have required to replicate a lot of work unnecessarily.