Only example I've noticed is Thunder Locus by the ember mage. SynergiesMod adds to each tier, the ability to 1,2,3 extra thunder locus in addition to the bonus already in the tiers. In vanilla torchlight 2 and with essentials loaded, the tiers just enable the locus to attack multiple enemies; can only summon one at once.
I like a lot of the changes in essentials, and looking through the list of what the mod brings, im not sure what might be adjusting the skills. Nothing suggests this. Im curious if anyone else might know what it is.