Why purchase from a boutique rather than bal.com?

I think the answer is pretty simple, because you get to pick which bag you want. You get to pick which leather type (since there are so so many types) and ultimately pick the bag that is the most YOU.
 
Not all colors are always available through the website. Like you may have noticed that they don't have the RH outremer or any 10 GGH bags. They didn't have the SGH Argent back in 08 and as for the 09 colors they never had the f/w bubblegum or noix.

I like the website 'cause if you don't like something you can get a refund (Bal botiques only give you a store credit).
 
The website also doesn't carry every style. There are no Velos on there and I don't believe there are any Firsts, Couriers, Mid-Days, etc. And as others have said, they don't carry every color in the styles that they do carry. I think people buy a bag from wherever they can locate it. Sometimes it is a real challenge to find the bag in the color/hardware combo that you want. And then you order it and just hope for the best as far as leather thickness, distressing, color saturation etc. Of course finding the bag in person is ideal, but not always possible.