Applying to a Math PhD program which doesn't require GRE as a physics/math major
I don't think it will prevent you getting accepted.  I followed a similar path (Physics + Math BS, Physics GRE only -> Applied math PhD).

But I recommend that you decide who you would like to work with in the places you'll apply to, and write them a very polite, short e-mail explaining your qualifications and interest.  If a faculty member is interested in you, GREs won't matter at all.