i have a two guitars setup with identical pups like a vintage strat would be. one with the hendrix pups which are all the same and another strat with three pups i wound that are the same. I do always put a tone control on the bridge pup though. its a very usable setup but i find it works best if you are adept at using your volume and tone controls on the fly. you can adjust the pup heights so there is volume balance but the bridge pup is going to be pretty thin on the bottom no matter what you do, which doesnt have to be a bad thing.
i also have a few strats that have pups that are similar but not exactly the same, like the classic stack+ set. each pup is different in the set, the neck and middle are pretty close. the bridge is definitely hotter and darker than the neck for example, but not so much so that it sounds like a different pup, but a little to compensate for the tonality of the position. its a great set, though i do prefer the stks7, vintage hot stack, in the bridge. the antiquity sets are terrific, but typically people get the hotter bridge. they arent all that much hotter, but they do have a bit of high end rolled off.