I don’t think, that this has changed.
If my memory serves me right, there was already a link to an instruction on how to root the phone.
The one thing that has changed is, that they no longer offer service and warranty for errors and faults caused by changing the OS.
And I really understand that, as there are so many things that con go wrong this way; installing another OS and apps even might brick your phone (please correct me, if I am wrong here). Fairphone naturally does not want to get into arguments what was caused by changing the OS and what is an error of the phone, as that most likely will be hard to tell or not to clarify at all. Therefore it’s a simple and clear rule.
My guess would be, that the “Fairphone Open” thing was something they developed and tested like the modularity.
With modularity they changed the design and concept (screws instead of clipping) to achieve the desired result.
With “Fairphone Open” - my pure speculation - they realized, that they invested heavily in this OS, needing lots of personnel, while a mere 5% of the users used this OS. And that is - with FP1 and FP2 to a great extent a special privacy and tech-oriented community and not the mass market. Since the FP3 is aimed at the mass market, they surely need all their personnel for service, support and maybe starting to develop future devices (e.g. a phone for the US-market). Developing an open OS for just max. 2% of all customers therefore would have been pure luxury, they can not afford, not yet at least. (Just 2% as I guess, that on the mass market the interest for an open OS is less than it is in the Fairphone community right now.
Well, that’s at least what I would expect to be the case, but it is of course nothing but speculation.