The pump gears may
not be damaged if the converter is not seated properly and the engine doesn't turn or run.
As to why it can all be bolted up....
The flex plate does just that... it flexes and allows everything to be tightened up.
But that same flex is pushing hard
on that mis-aligned pump gear.
Those gears are sintered metal.
Basically metal powder mixed with a binding agent/glue and heated to fuse it all together.
They are tough but relatively fragile.
Put enough force on them and they crack or shatter.
You really do need to inspect that pump... or... do ya feel lucky? well do ya punk?
Seriously, look close at that inner pump gear, make sure it's ok or you'll be pulling the trans again.
Edit; also check the T/C hub closely.
If there are burrs or marks, polish them out or carefully knock them down with a file and then polish.