The FSM states to put the ring in at the bottom and shows pushing it to the top with a piston to check ring gap.

I misread and thought it said to push it to the bottom.

As such I did all the ring gaps at the bottom of the bore. Of note this is on a used engine that is just at service limits for taper. So in essence, it's my believe the tightest part of the bore will be the bottom due to the most wear being at the top.

If I set my ring gaps to spec at the bottom of the bore of this used engine after a light hone, will this be a problem?

 

Nah, won't make much of a difference. Send it.
If it really bothered you, measure the gap at the tops of the bores. I would be shocked if there was more than 0.001" of difference.

 

I pushed the rings from the top down, letting it settle in the middle of the cylinder sleeve for measurement. 190 psi across the board on a D16y8 isn't bad at all. LOL