It can be so stressful when shopping for a new bike. Just go with your gut on this one. If you like the 2nd shop better and feel like they're leading you the right direction and you like the mechanics/salespeople/owner then go for it. When you buy a bike, you are buying a relationship with the shop. $200 won't matter if you don't feel comfortable/happy with your shop IMO.
I guess a 52 wouldn't be outrageous for a 5'3" person, but yowza! I have short legs and a short torso and my 48 fits me perfectly (but it's not WSD, so that might make a diff). I've ridden a 47 and have a 49 touring bike that's a bit big. I only wish I had the length to ride a 52- it would've made buying a bike allow me so many more choices.

Good luck with your decision, and make sure you let us know what you wind up choosing.