Yes, and no.
Yes, you can play Alexander with RTW's exe, but you have to trim down DMB because it's over 250 entries. The same with BI's exe. As for the campaign, you'll need to edit some stuff too, like mercenaries and ai_do_not_attack_faction line.

I can't tell if there's any noticeable difference. ALX is pretty much RTW with some extra features (and higher DMB cap). If you're not using any of the features, then I doubt it'd be any different.