I think the issue with Dipplin Evo being like Bloodmoon Ursaluna is that Bloodmoon is just a different form of Ursaluna while the apple is a brand new mon entirely - so it ocupies its own slot in the national Pokédex (as opposed to Ursaluna where getting the normal one is enough) and also causes Dipplin to be eviolite compatible.
It’s comparable in that both cases are something they’ve never done before. Prior to The Teal Mask, they had never had a regional Dex that included only the final form of an evolutionary line (be it a gimmicky new form or otherwise). Applin3 having a lone slot in the Blueberry Dex without Applin and its evolutions before it would be equally unprecedented.
Applin3 having its own National Dex number is irrelevant, because regional Dexes are specific to the context of that region —
especially as of Scarlet & Violet which, in contrast to the way the Galar Dex handled things, require you to have a
specific form of a Pokémon in order to unlock its entry (owning a Johtonian Wooper doesn’t register Wooper in the Paldea Dex, owning Red or Blue Basculin doesn’t register Basculin in the Kitakami Dex), and exclude evolutionary adjuncts that stem from forms that aren’t found in Paldea, like Quagsire and Perrserker.
(Plus, Gen 9 has already run roughshod on the National Dex in its own way — Dipplin is going to be at least six spaces removed from its own evolution despite them both being added in the same generation, while Walking Wake and Iron Leaves will be even more spaced out from the rest of their respective trio mates.)
It'd be pretty awkward for future games if Dipplin kept eviolite but couldn't be able to evolve because the evolution is "special" in the story.
I’m sure* it will be able to evolve in future games. I think whatever special status it might have will just be specific to this story. Sort of like how Sun & Moon explicitly stated that only three models of Type: Null had been created, but then Sword & Shield turned right around and said, “Oh look, some industrial espionage happened and now there’s more Type: Null.”
Personally, all I’m really thinking is that Kieran will be the first to have discovered this evolutionary possibility for Dipplin. Whether it’s dependent on Dokutaro or the Terarium or something else, I don’t know — I just think him being the first to discover it and him being battled at Blueberry Academy will be enough in-story justification for it having a slot in the Dex independent of the rest of its family. It’s the player’s Pokédex, after all.
* Well, assuming they don’t treat it like the new Hisuian evolutions. After all, Stantler and Ursaring can benefit from Eviolite in SV, despite not being able to evolve.