Once I get everything back together, I like to bang the shoes back and forth with the heels of my hands to help things settle in and center.
Agree, look closely at the pistons and those cups.
You should be able to remove the rubber cups without exposing the system to air, unless the pistons are already past the end of the bore.
The MC likely has a retention valve to keep residual pressure on the rear. because of this, you likely can't just remove the MC cap and force the pistons back to where they need to be. Using the bleeder will probably be necessary, unless you remove one or both pistons and then re-bleed that corner.