That's a pretty common problem- - - - -and I've been fitting pistons that way for a little over 50 years! You're on the right track by concentrating on the bottom of the holes. Don't worry about maintaining a good cross hatch pattern until the final few passes- - - -it won't hurt to let the hone spin at the bottom without oscillating until the hole is almost the right diameter. You can also put a short piece of .001" shim stock between the bottom of the honing stones and the hone assembly to preload the bottom of the stone a bit. I learned early on to bore the cylinders to the exact piston diameter, and put the specified skirt clearance in by honing. That's plenty sufficient to eliminate any machining marks left by the boring tool. If you happen to have a carbide "button" hone available, running it fast with motor oil as a lubricant and moving it up and down rapidly puts a very good cross hatch for ring seating in the cylinder as a final operation. It won't enlarge the hole at all. Have fun!
Jerry

"It is better to be silent and be thought a fool than to speak and eliminate all doubt!" - Abraham Lincoln
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