If EAA is going to work on it for you, then let them do it.
fwiw, having the coveversion work on 1 lower is doable, but then adding 1 or more lowers you start introducing possible issues. So again, if they are going to do the fix, just be happy.
I have some of the conversions and uppers in the RF and CF and some dont fit OTS. They recommend you send the lower(s) to them to fit it and i can see why. Just like CZ 22 conversion is made a bit tight to fit the lower, im sure the EAA may do the same.
If there is some mfg defect then add a note into your return, remember that pictures are worth a thousand words and if you can, use a marker to mark where you think is the issue or use some tape and put an arrow to the area.