@shylock since more or less every videogame supported by retropie is in 4:3, you're always going to get borders on the top and bottom (rather than the left and right that you would get with a 16:9 display. integer scaling won't make a difference.
with vertical MAME games it would be a nice fit, though: smaller borders on left and right than (un-rotated) 4:3 or 16:9 screens.
you'd also probably need to get a custom emulationstation theme done, unless someone has already done a square one, otherwise it's going to a look a little funky it think.
no idea about the performance...