In my experience . Maybe. Changing platforms should not change the amount of pressure exerted on the outside of your foot unless the carbon shoes allow the fitter more adjustment options. Sometimes the case with 2 bolt shoes vs 3 bolt. Your old shoes could be worn to the point of not supporting your foot . In this case new shoes can make a difference. Did he look at your old shoes while fitting the new ones?
I think you are going in the right direction by having a fitter make cleat adjustments. Wedges and shims can also be used to correct imbalances. This worked for me. If you recently made these changes, your foot may still be irritated. It can take some time before it heals.
I’m coming from Lake wide road shoes with G8’s to a Bontragger soft spin shoe with 2 bolt cleats . This was due to me having a stress fracture on the 5th metatarsal . Too much pressure on the outside of my foot cracked the bone. Some times riding thru pain is not a good idea. 
Hopefully soon I’ll be back in my pricey road shoes. They do wear out cleats when hike a bike on gravel.
Good luck with the foot.