We also don't know what Vulture's real agenda is in this reality. In "Homecoming" he just wanted money - now he has some kind of agenda against Spider-Man, but what does that entail? (and why would he think it was Spider-Man's fault anyway?) The universes must've merged or something, unless Morbuis took place in a universe with Spidey and it just never came up.
I honestly doubt they had any idea where they were going with it, but what would Morbius's motivation even be for teaming up with Vulture against Spider-Man? If it happens, I'm sure they'll come up with something, but I'm opening up the floor for speculation - what would make sense?
Who is Spider-Man in this Universe anyway? It's not Tom Holland.
There came a time when the Old Gods died! The Brave died with the Cunning! The Noble perished locked in battle with unleashed Evil! It was the last day for them! An ancient era was passing in fiery holocaust!