Soooooo it turns out that I posted this late at night while I was concentrating on getting my daughter to sleep after looking at Missing Score's damage calc for about three minutes and guessing that C4 was a copy of 48 before the Morph reduction is applied. Turns out that's not the case.
The Morph damage reduction occurs in command function 1C and the copy occurs in command function 9 which is always executed at the end of a damage-inflicting command.
If you followed that explanation then good for you. If you didn't, I'll sum it up by saying I was wrong and Missing Score does take the penalty. I didn't document it's power equation right and it's actually
1 + (Power * AP / 10000) / 16
instead of
1 + (AP / 10000) / 16
like I had it on the wiki a while ago. So there you go. Power does factor in to the strength. At high levels of AP you won't notice it. With 2187500 AP you'll always do 9999 damage when trying to morph a morphable target.
Conformer doesn't take the penalty and Death Penalty is second best for morphing at its weakest. DP has a lowest morph power of 10 while others' ultimate weapons have a max of 7.