Also what about the buff setup ie raging strike, hawk-eye, etc... once auto-attack kick in-between actions you wasted it.

IMO

Auto-Attack = Rise of the BOTs
Your are mistaken to think that this will have any effect on bots whatsoever.

Secondly, FFXI had similar buffs that would apply on next hit and auto attack. The seemingly simple solution was to create a delay before the next round of auto attacks, giving the player plenty of time to initiate the next weapon skill before attacking.