The spray foam will seal it so no air gets in so it should be fine.

The key to proper air flow is a sealed vent; foam works well but don't over spray. PLEASE wear gloves and a full face mask because that stuff is a bear to clean up and NEVER get it on your skin.

If your cover for the unit does not cover these spaces, there are metal strips intended to cover the seam in a floor where different floor coverings meet with screw holes already drilled. Measure how much vertical length you'd need for all for sides and invest in what you need to cover the edges. These are available in most larger hardware stores and the big box building supply stores (Lowes; Home Depot).