I think what is meant here is that if you move the brake pads closer to the rim (hence “shorten the free stroke distance” of the brake levers), you need to keep the wheels in good alignment to avoid brake rubbing (“the spokes of the wheels have to be adjusted by bike shop more often”). Hence the OP decided not to adjust the brakes tighter/closer to the rims.
This said, I agree with @mcneese.chad, there are signs of frame sizing issues here, as well as some strange fitting concepts - you do not move the saddle to get closer to the bars, unless the saddle was in the wrong place to start with.