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To give an overly detailed explanation, the advantage of 650b wheels is that you can achieve the same wheel diameter with a much wider tyre. A 650b with 45mm tyre is very nearly the same wheel diameter as a 700c with a 28mm. So you get the advantages of a much wider tyre - more comfort, better traction, etc. - without significantly affecting the bike's geometry and handling in any way.
However, some frames don't have any extra clearance at 650b tyre diameters. If you don't have the clearance for a 45mm 650b then your bike's geometry is going to change; the BB is lower, the trail is smaller, etc. compared with the 700c×28mm (or whatever) that the designer expected. Some frames have bent stays and so on that mean that clearance is effectively the same at 650b/700c.
What would prevent 650b compatiblity of a frame designed for 700c, like the Trek mentioned above? 650b is just a smaller diameter wheel, no?
edit: talking about a frame with disc brakes