Effectively just what the title says. The berries that are missing seem to be the poffin-specific berries, which seem to be BDSP exclusive as SwSh seemingly didn't have them. They also don't even show up in the bag list in PKHeX, so I can't manually increase the number of the ones I have either. These include Bluk, Razz, Nanab, Pinap, Wepear, Cornn, Magost, Rabuta, Nomel,
(Ignore the berries that aren't at max, spent some on stickers)
As you can see, the previously-mentioned berries aren't in the list, and can't be added to the list/manipulated in any way.
Hopefully this is useful!
(As an aside: I've really appreciated using PKHeX over the years, yall are doing a great job!)