I reckon you just get used to whatever you have, within reason.
Partner has a flipped stem and no spacers, which helps keep the front down.
Bike was set up for her by the Dales Bike Centre after she had a few issues on really steep climbs on a skills course there – she loves it.
I have the stem the ‘right’ way up and spacers, same size & geometry frame.
I don’t mind either tbh – feel more confident on the downs on mine, but both are comfy and seem to fit fine.
Find I’m more sensitive to crank length, reach and seat height tbh.
As long as I’m comfy, it doesn’t seem to matter on an MTB.
Much more critical on road for me, takes me yonks to get comfy on a road bike, not as much shifting around I suppose.