I’m definitely no expert; but I assume that it would depend on what the organism so modified uses that base pair to code for.
Conventional organisms can, for the most part(and if one can’t there’s probably a symbiot or scavenger that can) chop up any protein they encounter, which covers all the ones(not always the same species to species) that are coded for by existing base pairs.
Unless the new base pair also includes a quite novel protein to code for, the organism attempting to digest it probably wouldn’t even notice. Even if it does include something quite novel, being able to disassemble your enemy and turn their amino acids into you is a core skill, so a protein that resists digestion in general (especially if it does so while remaining useful to the organism producing it) would be pretty impressive on its own.
