There is a HQ box on the auto synth screen, so it should be possible.
I have only ever had 1 HQ from auto just making base mats, so the chance really isn't great.
I have also had a failure on auto where I could have had 100% guaranteed success doing it manually.
So if you actually want Exp, Success, or HQ, you are better off manual.
Of course you may just be after some easy AFK Exp, and if you have the money to burn, go for it.