You (should) drop your heels more with flats and so that usually more than accounts for the extra stack. I generally lower my saddle a few mm if I put flats on the MTB
I ride midfoot so I probably do a lot less heal movement than you tippy toe riders. It still makes no sense that your pedaling would change so much just because of the platform, certainly not enough to make up for the maybe 5-10mm difference in stack between clipless and flats.
You (should) drop your heels more with flats and so that usually more than accounts for the extra stack. I generally lower my saddle a few mm if I put flats on the MTB