Ow, I'm confused as to what I should be responding to.
I did notice the thing about 'What if the locals have their own protocols?', though, and in lieu of blinking confusedly will try to answer that.
I think that the Federation, because bureaucracy tends
to fall into this trap even when they shouldn't, probably plans for a situation like they faced when they
were the ones who were the locals; Which, in the human context, means we might have reasons to think there are aliens, we might even have notional plans for an alien contact (done by the same folks planning, for example, wars and other crisis responses, either as a training exercise or because things got slow at the office one day), but those plans weren't designed for real implementation in any case, are never updated (let alone exercised), and are utterly useless...All because even if logic suggests there might be aliens, nobody really thinks (or is likely to admit they think) it's at all likely. Until, of course, it happens.