TECHNICALLY yes, but think of it from this perspective: outside of Titan Gas, you're running around DPS'ing adds. If you have one split on each boss in order to "cleave" your damage, then not only are you doing 60% less damage to the adds (which are the of top importance for DPS during that phase) but your clones also won't attack if you're running around not attacking.
Likewise, when it comes to Titan Gas and you actually get to go nuts on the bosses, it won't matter if you summon one clone to hit the one you're on, or one clone to hit the other one, or both clones for one boss each, or both clones on the one you're hitting - you'll still end up with 20% extra damage done.
Not that an extra 20% damage is a bad thing, of course - you just can't leave it up while hunting adds without gimping your own damage on Strengths/Courages, and it makes zero difference how many clones you summon or which boss they're hitting when you do get to use them.