It's cutting edge-level minor differences, to be sure. But in the hypothetical, stacking too many MCH (defined as: enough to lose 1% stats or more in party bonuses for not having one member of each role type in the party) just because MCH does MNK-level damage is still a dps negative; at most you'd see 2mch / 1melee / 1caster, perhaps, and the implications of that are up for interpretation. Last I checked as well, double stacking jobs still comes with a penalty to LB generation which itself hurts dps, but it's not as immediately noticeable.
