I think you're right that people do tend to use "AU" as shorthand for "total AU," although I notice in exchange sign-ups, many people will explicitly note that they're okay with canon divergence when disallowing AUs, so I don't think the two categories have been completely divorced.

Crossovers and fusions tend to get grouped together--crossover exchanges, for example, often allow fusions as well. However, I agree with others that they're not really the same thing. Having an unexplained spatial anomaly bring the Enterprise and Galactica together for an unexpected encounter is a bit different from making Apollo a lifelong Starfleet officer instead of a colonial pilot.

Personally, I love crossovers and rarely care for fusions. I generally prefer characters to be who they are in canon, with the same backgrounds, which fusions tend not to have. Crossovers, on the other hand, play into my love of outsider POVs. They're often an excellent chance to see characters from one fandom react to characters from the other with an outsider's eye.