I am collecting parts for a 29'er mtb build. The dropouts I am thinking about using are Paragon's with low-mount disc brake mounts. Now, I know clearance can be an issue, but I know that either of the brakes I plan to use will fit. What I'm wondering though, is what is the advantage/disadvantage to this style of mount? I want to use them strictly because I think they make for a cleaner look of the completed bike, but other than that, is there any reason from a structural standpoint? Thanks!

Structurally, the seatstay mounted brakes (using thicker tubes and/or a brace) work just fine and are in use on thousands of bikes- from an engineering standpoint, it makes more sense to mount the brake on the stronger chainstay. So, strengthwise, it's really a case of "strong enough" vs "stronger than that"...there are a lot of things in framebuilding like that.
So, the good and bad I've experienced with cs mounts:
pro-
cleaner look
the best way to have horizontal drops w/discs
the caliper body is better protected in a crash
the brake won't interfere with rack mounts

con-
the downtube brake cable routing is kind of ugly
not all brakes work (like you said)
won't work at all if the rear triangle is too small- check before you put the seatstays on!