Not sure I understand your concerns?

Are you sayingt that, to take your exemple, the PUG would use a buff to say "increase damage of the next attack" and that that buff would be consumed by the auto-attack? Is that your concern? If it is.. then there is no reason why they cannot make the buffs that affect the next attack not applicable to auto-attack and by doing so not consumed by them.

Did I get it right or I missed your point?