1. She has the smallest size - 44 cm - which is exactly what all the fit calculators recommend. But the stem that the bike shop gave her - and that the fit calcs recommend - is only 70mm! Is this normal?
The website lists the stem length for that size frame as 90mm. I'm guessing the shop that fit her decided she needed a shorter stem. Like snicklefritz said, if it is not so short that the bike handles poorly, it is a good thing if it fits her better than the stock size.
2. It looks like the brifters are regular 105s instead of the special short-reach ones that are available, and that other brands (Giant, for ex) put on their women-specific design. Is this correct, and is everybody comfortable with them?
The brake levers on my GFs bike are definately short reach. I considered stealing hers as I have short fingers, furthermore, she doesn't go fast enough to need brakes anyway. (just kidding honey 
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3. The bike came with 42 cm bars! Hell, I can use those and I'm a 5'11'' male. Is this the norm as well? Seems like the teensiest frame available would come with 38, or 40 at least. The fit calcs recommend 38 for her.
The specs on Specialized's site list the bar size for that frame as 380mm. I think the correct way to measure that is in the "drops" from center to center". That being said, I'm sure my GFs bike are 400mm like the specs list. They seem teeny to me.
4. The bars have this big puffy wrap, or at least puffy stuff undet the wrap. It seems to me that a small person with small hands would want fairly thin handlebar/wrap diameter. Once again, is the the bike spec, or something that the store put on the make it more "comfy" and sell-able?
I'm sure it's about the comfort. One of the biggest complaints my GF had was that here hands hurt when she rode her old Schwinn.
5. Finally, are the seat and wheels decent, or are they calling for immediate upgrade? Alex 295's are the wheels, I think.
I think a saddle is such a personal preference thing, that I'm suprised that they aren't an "option" on good bicycles. Having said that, the saddle on her bike is decent and it seems to follow the generic guidelines for womens saddles. i.e. wider sit area, shorter nose, center cutout.
As far as the wheels go, I'm no wheel guru. They seem to roll fine, and we have had no problems with them
Mostly just curious about the normal bike spec, and what we might be able to insist the store swap out. The store is Hudson Trail Outfitters, by the way, an REI type store. They are supposed to have a 100% guarantee, but it apparently doesn't apply to bikes.
PS I told her the Giant Women's bikes were spec'ed better at the same price point, but it went in one ear and out the other, apparently. Didn't even get a look.
I was not aware that Giant made "Womens" bikes. Is that new for this year? Seems like last year, all they had were small "mens" bikes. Most women I've talked to do seem to feel that some of the bicycles designed with them in mind do fit better.