I just un-clipped my Hubba's body from the fly, from within, or inside of the fly, with the fly attached to poles.
Its doable, but I would only do it, under downpour conditions.
Tried to do this in reverse setting up fly and poles (without a footprint) which is nearly impossible, and a good way to potentially break a pole.
I'll need to practice, but I'm pretty sure that I could have the inner tent folded inside the fly, lay them out, and slip the pole assembly between the two, which would keep inner tent dry,(during rain) and possibly erect the inner tent, to the poles while still being covered by the fly? Time to tinker now.
If the fly is wet, and packed separate, then you would need to slip the dry tent body under the laid-out fly, and still erect, like I already mentioned.