Short answer: It's a complete mess.
On the surface, the path of ownership went Commdore->Escom->Gateway->Amiga Inc.
But Amiga Inc, rather than being a singular owner, is actually a long series of shell corporations and quasi-legal entities so convoluted that it would probably take the full faculty of a major law school several years to decipher.
Hyperion was licensed to develop OS4, but a provision of the contract (the "bankruptcy clause") was to grant them full ownership if Amiga Inc went out of business. Whether that clause was properly triggered, amongst other issues, was the subject of a multi-year lawsuit. From my understanding, the outcome is that Hyperion now owns OS4 outright and has a license to use and distribute OS3 and earlier in matters related to OS4.
3.5 and 3.9 were developed by Haage and Partner, and I don't think there are any ownership issues surrounding them. (Not of this type, at any rate.)
Cloanto can trace its license to Commodore and the Escom/Gateway era, so it's also protected from the more recent insanity.