It's possible that the "servers" that Eternum (the VRMMO) has are worlds that are already dead so it's easier to lay claim to it. The worlds that're inhabited on the other hand are like the world Orion and co come from and H'yliar, the latter implied to be outside the Founder's influence.
Based on what we know, every server has "rules" of sorts which allow certain things to be possible. For instance, some servers allow magic, while some don't. I don't think the Founder or Ulysses made that system, but rather that's just the rules of that particular reality (just as how our reality has "rules" or "laws," like gravity having a constant speed), and that the only way to break them is to utilize items or magic that can "overrule" the rules of that reality (such as Orion's powers and the Weapons of Atlas).
As for how astral projections can cast magic...well a projection is technically a being of Eternum, and beings of Eternum are shown to have affinity to doing feats not limited by the rules imposed by one's physical body. My current theory is that a projection essentially "mimics" what an inhabitant of a server would be like, from the abilities that an inhabitant of said server would have down to their form (i.e. Nova's and Alex's projections being Pixar-fied in the Pixar server). This, however, doesn't apply if you bring your physical body in Eternum, as your body is still bound by the "rules" and "laws" of where your body came from (the real world), and not the "rules" and "laws" of the server your physical body is in (unlike the case of projections). And before you ask, yes, this includes the case of Orion...but then again, it's been foreshadowed for a while that his body isn't exactly "normal" to begin with.
As for the xenomorphs being a threat...well, the "threat" that they pose as explained by the story isn't so much as an existential threat and more like a threat where their sheer numbers would eventually render servers unplayable for the non-combatants. Not to mention this would cause issues with Ulysses trying to maintain the "masquerade" of Eternum being a VRMMO. And that's something the Founder wouldn't let slide since he'll want to maintain it until all the gems are found and collected by the millions of players searching for them at the moment.
Finally, with regards to the Founder...well, it should be pretty obvious by now that there's likely more to him wanting the gems other than for gaining godhood or divinity, especially since William never really did elaborate why giving the gems to the Founder will be "the end." I'm sure we'll eventually find that out, along with how the Founder intends to use the gems (or learn what they're really for).