In FGO, Altera appeared in Septum, was defeated and later summonable. In Extella she appears to be a major threat at the start and isn't by the end. Requiem has barely gotten started so who know what's going to happen there.
If you're talking about future possibilities, than it is not a trend yet and thus can't be used to excuse arcade.
The Epic of Remnant chapter that gets mentioned is Shimousa for having Musashi, Douman, and being a pseudo-Lostbelt. Maybe Salem for introducing Outer Gods. It would be silly to say Shinjuku and Agartha are utterly irrelevant because they don't get mentioned afterwards so the same should apply to SERAPH.They're canon but utterly irrelevant. The writers never reference them outside other events and that one scene in Solomon. Handwaving the lack of one of the Beasts is just that easy, all they need is an event about it, or a throwaway line on the LB equivalent of the Trash Heap.
You can't compare Beast VI to be missing to Beast III being a sidequest because a mobile player will still fight Beast III. SERAPH is in the main interludes and Ooku will most likely be added after a year or two. Assuming the exclusive thing goes though, a mobile player will never fight (all of) Beast VI. If there's an event about it, then it wouldn't be an exclusive, but if there's just a throwaway line, then that's just bad storytelling.