If "all" = "all" that's a big boost. I would personally rule that they don't stack, but that the highest one does apply. I can see the argument for this aspect, but it's not one I'm a super big fan of. That said, 6e has evolved what's possible with magic, and leans towards more permissive.
In my mind, whatever the logic is that is used, it should mimic whatever happens to an adept when they use the Matrix. I'm not sure this interpretation does that. Do adepts get ref boosts in VR mode too? There used to be a hard line between "worlds".
If I was running it as a GM, I would rule the bonuses from physical abilities don't apply, but mental ones would. I'm assuming here that "all" = "any that would reasonably affect astral stats" (which would disqualify Improved Reflexes since that's only the physical body).
That's just my opinion based on prior editions. I defer to the errata folks and other experts for 6e.