Nope, not using an Apple Pencil. I took it out again yesterday to practice - it was at around 60%. Today, I opened it up and it's at 35%! Checked the battery over 12 hours chart and it showed basically the same steady decline in the above screenshot.
I had iGigBook (basically a PDF manager for sheet music) running the whole time with the same chart pulled up (as it was asleep, too). Maybe it's doing something in the background, I have no idea.
It's probably a problem with iGigBook, and I can report the bug to them. It's really not that big of a deal after all - I can just close iGigBook when I'm done using it, that seems to be the solution thus far, just annoying to see how when I'm not using the iPad the battery drains somewhat quickly.