I think you're 100% right about the chip damage, I hadn't even considered that. Thanks! That makes a lot more sense than some random hidden modifier.I tested with Taki and there seem to be 2 categories:
1: Attacks with scaling, for Taki i found 4:
PO B+K, PO B, WRO K and the worst is 3B.
After which her CE does 64 instead of 90 damage.
2: Attacks without scaling.
Here CE does the normal 90 damage.
BUT in both cases, if the crushing attacks do chip damage, because of Mekki-Maru or Soul Charge, this is added to the total damage.
With Stalker B crush (10 damage on block, no scaling) into CE doing 100 damage for example.
I assume this is the same with your X in Soul Charge.