When a fighter selects the Versatile Training option, he uses his BAB in place of his ranks.
But, what I want to know is, does the fighter still receive the +3 bonus for now having 'ranks' in that skill?
Yes; they're actual ranks, rather than a +X bonus, so they count for getting the class skill bonus.
The Fighter will always get the class skill bonus, by the way, because in addition to granting ranks Versatile Training also makes the selected skills into class skills if they weren't already.