The "alliance" was done a couple years ago basically so they could get a better deal from component vendors (electronics, plastics, wheel parts, bearings, etc.). The KX250F and RM-Z250 were the only models that were jointly developed IIRC. To help differentiate them, I think they also used different shape radiator shrouds.
Other bikes that were basically identical included some smaller ones (KX65/RM65, plus a few others) and at least one ATV (LT-Z400/KFX400), but all those other models were pre-existing in the line-up of one company and adopted (with different colored bodywork, of course) by the other company.
As for the racing programs, both companies maintained complete separation.
But I believe that both companies feel the benefits of the alliance have run their course and are going to dissolve it in the near future if they haven't already done so.
(Edited for clarification.)
ETA: Suzuki has done this sort of thing before, though not to this degree. It has sold engines to the old (now defunct, I believe) personal watercraft company Wet Bike, as well as Bimota. Also, Arctic Cat uses the LT-Z400 as the basis for its 400cc sport ATV, which is available in two or three colors.