Should I remove all of the spray foam surrounding the 2” polyiso that sticks out, so that I can install Thermax flat against it or it doesn’t matter much, save time and spray foam in the additional Thermax regardless? 

I had 2” foil faced polyiso installed on my rim joist.  I would like to add 3.25” Thermax for additional insulation but also to cover the transition from the Thermax on the wall up to the rim joist. Does the air gap matter which would be created if the Thermax wasn’t perfectly flush against the polyiso?