You can align to stock specs with the MM plates if you wanted. The MM plates just correct a few issues when you lower a stock fox and can't align back to stock specs. But once installed there is nothing preventing you from doing a stock alignment on the car with the MM plates.
MM recommends some different specs in their install directions, mainly dialing in a little extra caster which is lacking on the fox cars. You may want to consider aligning to their specs or even adding in a bit more camber depending on your driving style.
Bigger issue is finding a shop that will align to anything other than stock specs for liability reasons.