Did a simple test. Last night, before reset, I took screenshots of every row in my Details meter to see if this 3% buff included pets.
Does it affect pets? Yes. They finally did that right this time.
Is it still messed up? Yes. They forgot to include Auto Shot. All of my abilities are doing 3% more damage EXCEPT Auto Shot, which is doing the exact same damage as the day before.
Minor maybe, as Auto Shot is typically 6-9% of my overall damage, but still an oversight.