Yeah I never liked that Resurrection took place so far in the future compared to Alien 3, because it definitely felt like they threw out a lot of the world building of the original films only to replace it with......nothing that looked like it was that much more advanced than anything we'd seen before anyway.
Plus it makes you wonder what the hell the Company (or United Systems Military) were even doing that entire time if it took them two entire centuries for someone to finally say ".......so, cloning Ripley, then?" as their way of finally getting hold of an Alien.
But yeah I just think it'll more than likely be some contained, isolated story that doesn't even have to feature Weyland-Yutani in any capacity, nor even particularly explain where the Alien/s that are going to be in it come from. Just have some rock miners haul in a large meteor that has an egg on it or something, or some planet excavators dig into some cavern on a random planet and find a few in there. It's not like the original films ever gave us an answer to where the ones on the ship came from to begin with.
And yep, I also never bought the argument for not having any Alien films set fairly soon after Alien 3 because is meant Ripley's sacrifice was for nothing, when A) Alien 3 already makes everything Newt and Hicks went through in Aliens count for nothing, and B) one of the things a lot of people seem to like about that movie is that it's so bleak. Why not go "full bleak" then and say her sacrifice was for nothing? You can't get much bleaker than that!
I like the way the RPG is handling it where a few years after Alien 3 they're not so common that they're popping up on every planet now and the Company has all the Alien samples they could want, but they're certainly still out there.
Plus if you set it in that kind of time period, Alien Resurrection is still so far off that you could just make up whatever head canon you like about why there weren't any around anymore at that point in time that they felt the need to clone Ripley to get some. It's not something you'd even need to address.