No, I've never swapped bookshelf speakers between systems. I listen to a system for an hour or two every day & then switch to the other one each day so I'm very familiar with the differences in sound signatures.
My M2s/EP400s are placed in a window alcove parallel to my listening couch about 10' apart & 11' in front. The M3s are mainly for an ambiance (party?) system & are placed about 25' apart diagonally in opposite corners - certainly not textbook. My M3s needed to be tweaked before they sounded really good. Because of the corner placement, bass reinforcement was excessive causing me to EQ the bass way down (other brands of speakers did the same thing there), but it still wasn't right. So I tried plugging the rear ports, returned to a flat EQ to & voila, all unnatural reinforcement & muddiness were gone. Great sound now.
Because the EP400s are powerful & accurate with 8" drivers & the way that the M2s roll off naturally below 70 Hz, I think that the M2s are a better match to the subs for music. I guess that what I'm trying to say IMO, is the driver complement of the M2/EP400s' - 1" tweeter, 5.25" woofer & 8" woofer - is probably more pleasing & easier to tweak than a M3/EP400 complement of - 1" tweeter, 6.5" woofer & 8" woofer.
Then again, maybe I'm full of it, ha!