Just in case anyone reads this: I restored my Dolphin save to a physical memory card and tested this on hardware. The issue remained. This means either Dolphin did something terribly wrong to the save itself, or giving myself items in PKHeX was the cause.
EDIT: Dolphin's savestate workaround actually let me work around this issue, though, despite this being totally unrelated to savestates, which I never used
EDIT: Dolphin's savestate workaround actually let me work around this issue, though, despite this being totally unrelated to savestates, which I never used