Well the simultaneity issue is solved by, if you have p_h p b > p b p_h, converting them to, say, PH P B or similar container characters first and then doing the change. But really this is q inconvenient and I am pretty sure that the SCA could also do this. Some kind of simultaneity tag should be doable, no? Something like

=p_h > p
=p > b
=b > p

Idk how you would implement the notation but it would have to be something to make the SCA first transform all changed phonemes behind the tag into unique variables and only then resolve the changes to prevent overlap.