Before my surgery, my PCP was pretty determined that I stay on the name brand, rather than generic Protonix. He was concerned as you are. However one time it was refilled accidentally as a generic, and it was just fine, so from then on I took the generic version.
I would suggest that you read over this document if you haven't already. After taking PPIs for 15 years under the care of a PCP and a GI doc, nobody ever provided me with full information regarding how to take PPIs. This article does talk about taking the PPI in the morning, but that's not the important thing. Some benefit more from taking it before dinner, while others need to take it twice a day. The important thing to take away from the information is HOW to take it. See if it's helpful. I found it an eye-opener.
Nissen Fundoplication 2/09
"Whatever you fight, you strengthen, and what you resist, persists.”
“Worry pretends to be necessary but serves no useful purpose”
“Accept - then act. Whatever the present moment contains, accept it as if you had chosen it. Always work with it, not against it.”