Your both right up to a point, there aren't many games which use multiple textures for two reasons. One is draw calls and the other is shader use, apart from that even if all textures were to use the same shader, you would need to call the spec and normal maps as well.
What many of those new to uv mapping do is to use a third party unwrapper which will always unwrap and pack separate clusters (islands) into their own uv space, which means that each cluster needs its own texture space. You can in fact overlay clusters and the engine performs its own 'unwrap' for lightmapping which means a small texture can be used for a very large object without any loss of resolution.
Of course this wont work for every model where you may want a baked AO or whatever, but in general it's the best way to go, particularly for architectural models.
The main reason for multiple maps may be if certain parts of a model may be swapped out, such as weapons and hand textures, it was the only reason you had multiple textures for dynamic objects in Classic, that and the fact these were usually in the players face. Static objects should not require multiple textures (whatever the scale) in a game engine if uv mapped properly.
When you have a game engine designed for easy use by a whole bunch of individuals and not a game designed by a 'team' then it's really a lot on your plate to get perfect optimisation and the reason you wont see many Atlas textures for Reloaded media, when users will mix and match whatever they have in their library.
For us Artists it's a real juggling act and we have to be very aware when creating media for use by others, it's the reason Wiz is so uptight about it, so forgive him if he seems a little irate
Just an aside, but I reckon Reloaded should handle texture sizes up to 4096x4096, if anyone was thinking of creating their own media and Atlas textures for their own games.