I haven't lifted a 2nd or 3rd gen tacoma yet so I see what you're saying about the mount being in the way but as far as the body lifts go they do have uses in other applications, on my TJ Wrangler a 1.25" body lift and motor mount lift give you the ability to do a tummy tuck and get rid of the skid that hangs down almost 3" (better known as the shovel) and go with a skid that mounts flat up to the frame and pick up a lot of clearance. A small body lift also only lifts the body for tire clearance, like on my Frontier, and still have a lower center of gravity LCOG than if lifting the whole truck.
Make no mistake about it, Im not saying that a body lift is a be all of end all kind of lift, I prefer not to use them but they do have use. Most people do a 2" lift on their frontiers and have no trouble with 285s on stock rims, my pro comp rims stick out about 2" further than stock and I still had to do some trimming and melting with 5" of lift....... Couldn't have made it work without the body lift.