I’m not a ‘lore expert’ but I’ll try to answer as best I can.

Eos and Selene used to be separate pets with different unique abilities. However it’s also made clear that they aren’t two separate entities, simply two different manifestations of the same entity. The change to delete Scholar’s Summon II and turn her into a glamour was only in the most recent patch (more or less), and they don’t generally adjust lore when it becomes detached from the gameplay (i.e Astrologian cards all do the same thing despite quest dialogue specifically saying they have unique effects)z

Following from that, Seraph’s true ‘identity’ isn’t exactly clear. From what I understand, I think Seraph is the true ‘entity’ which Eos and Selene comprise. That is to say, they’re two halves of a whole, and when you squish them together, you get Seraph. But there’s no official lore to confirm to deny that theory (as far as I’m aware).

Scholar’s separation/non-separation from Arcanist is a tricky one which goes back to even before 2.0. They needed a new healer (otherwise it’d only have been White Mage), but they’d also spent a ton of time/resources and were running thin on both. So they decided to try having their newly added job as a ‘branching’ job that could go into either Summoner or Scholar. The problem was, because those jobs had a shared base, it made balancing the two extremely difficult. Either Scholar ended up being affected by Summoner changes, or vice-versa.

Then there was the difficulty of them having to deal with essentially two different spell sets squished into the one job. The result was Scholar ending up with a bunch of DoTs that were meant for Summoner, and Summoner ended up with a bunch of utility like Eye for an Eye and Physick (which still scales off mind even though Summoner uses int lol), and Resurrection.

As a result, they decided to simply separate the jobs toolkits as much as they possibly could. But because of ‘netcode’ or whatever, it’s simply not possible for them to remove
Arcanist as a base class from either Summoner or Scholar, which is why we still some of these relics (like the aforementioned Summoner Physick)