If it's a reboot, an "alternate timeline" isn't needed. It's a reboot.
The whole idea of a reboot is that it's cutting ties with the past. BSG and nuBSG are two completely different animals.
As far as making another AVP? Sure, why not. They screwed up with the first two, but hopefully now that new people are running the show things could work out for the better this time. The concept is still sound, and there is still the possibility of a great film out of the process. I'd say wait and see how the new Predator and Alien films work out though.