That is a frustrating predicament, and one that, at 4'11", I've been in at one degree or another since I started biking. Luckily, I'm still young and flexible and really have to be in a bad position to get pain on a bike. But even for me, perfect fit comes into play from a performance and endurance aspect (I WILL start hurting on a 60 mile ride if the bike doesn't fit me!).
I'm surprised the shops aren't willing to play around with stems and or saddles for you to test ride. It's a 10 minute swap for them (that includes swapping it back after you are done!). Perhaps being a little more demanding will help. Ie: "I really like this bike, but I'm not convinced of fit, can I please test ride it with a different stem before I make my decision".
The other way to handle it, which to some extent is what I did with my last road bike, is to go to a shop you TRUST that has a VERY good trained fitter (not just the standard seatpost up and down, stem adjust fitter).
Either go ahead and pay for the fit (not cheap unfortunately) as if you were going to get a custom frame and get your ideal numbers (it should basically come out as "here are all of the dimensions/angles/etc for a custom frame that fits you and your described riding style"). You can then compare these to stock bikes and find the one that is closest (the fitter should have some ideas for you as well).
OR find a bike from them you like that you think is close but not quite right as it sits on the floor and have faith that if they tell you it can fit without pain that it can (this is where having a good, experienced fitter on staff is key).
I did the latter. I knew the bike I wanted was close but bordering on too big judging from the test ride on a similar bike. I flat out asked, "Are you SURE you can get this bike to fit, not hurt, and not make compromises". The answer was "No problem I wouldn't sell you that bike if I couldn't get it to fit right". I ordered it and it fits great with their tweaks (but you have to really really trust your shop and fitter for this to work!!!).
You'd be surprised how much of a difference 20mm off a stem or 5* difference in stem angle can make (and different bars, etc, etc), but I understand the hesitance to buy something that expensive when the test rides aren't feeling right.
Be persistent, you'll find the right bike and shop for you. It just takes more time when you are not a standard size.