Finally figured this one out, and it was simple enough i'm annoyed at myself for not looking before. Each of the attributes does use animations to fade as Garkin said, so I looked into the metadata in ZGoo, found the timeline and was as simple as setting the alpha for the animations.
Lua Code:
ZO_PlayerAttributeHealth.playerAttributeBarObject.timeline:GetAnimation():SetStartAlpha(minAlpha)
StartAlpha for the player attributes is its 'resting' state, so this is the minimum it'll fade to, EndAlpha is its active state (ie, during combat). Have been testing this in my mod while I finish polishing it up and its working fine so far, and got rid of wibbly feeling about having to use OnUpdate to force alpha.