Guess what, many of today's frames from the largest bike Manufacturers are built in Asia. And not at a Trek, Jamis, Specialized, Cannondale, Bianchi, Soma or Surly, etc.... manufacturing plant. Even so, some frames are built and spec'd different by the bicycle Manufacturers. But of course, everyone already knows this.
And what about custom frames? How many people actually test ride a frame before deciding to buy custom? I'll bet most of these are ordered and sold (on-line) without anyone actually riding a similar frame.
So what's the big difference? ....it's about service and your own ability in determining what you need. Some people need help and others don't. A LBS is always a good option for people who can't or won't do the homework necessary to select a properly fitted bike.
My story.....May of 2011, I purchased a Schwinn on-line. It's a 520 steel frame with a selection of Shimano 105, FSA, and Tektro components and Mavic wheels. A bike with exactly the same components by a major bike Manufacturer (on a aluminum frame that rode terrible) was listed at the LBS for almost twice what I paid for the Schwinn. Needless to say, I've been extremely pleased and satisfied with my purchase.
In any case, it's nice to have options.....best of luck.