I think 1" standover is for road bikes, and 3 to 5" standover is for mountain bikes. My mountain bike has about .5" standover, a faux pas, i know, but i love the bike. So those measurements are guidelines but variable. If you will be riding really rough hardcore stuff the bike with more standover room will be easier to manuever and recover from crashes.
There is a way to judge if top tube length is right for you but I forget what it is. I think TT length is one of the main differences in WSD to men's bikes. I've been told Gary Fishers and Treks have the same geometry except for TT length. I tried several Gary Fishers and they all felt terrible to me. Tried several Trek's and liked them. (which sucks because Gary Fishers have way cooler paint jobs)
My wife is 5'4" and also has a long inseam and short upper body. She said she felt good on a 16" Trek 3700. we rode quite a bit. The bike fit fine but quality was an issue as we rode pretty rough stuff. So when it came time to replace it she went for a 16" Trek Fuel EX 7 WSD and said it felt worlds better. She said it actually "felt" like the same size, but just seem to make her back/neck/arms etc.. feel better, but her angles and breathing room seemed the same.
Oh and as far as savings, yes, sadly, men's bikes often have better sales because the stores buy more of them then need to get rid of them for new models.