I use SPD’s and a few pairs of different shoes all set up very similarly.. I get a pain in the outside of my foot perhaps an inch or so behind my little toe, obviously my shoes are pressing against the side of my foot (just the right foot). Seems my foot isn’t flat but tilted and this causes it. Would a platform spd help keep my foot more level or is there a better way to try for set up?

You could try different inserts that suit your foot better. Or to raise that side up tape a thin piece of card under the current insert just in that area.