In Spider-Man Unlimited, Spidey says Eddie's been for the symbiote for so long it has messed up his mind a bit, explaining why the two are working together and why they're more symbiotes than humans. SHIELD being there isn't too weird considering they showed up a few times in Spider-Man TAS and worked alongside the web-crawler. It definitely seems like an alternate universe kind of deal.
I'd say there's a few too many differences in priorly established moments in SU for us to assume that certain feats/events from TAS can be scaled to.