Yes, unless you choose to use very wide knobby tires and fenders to match. In that latter event, you'll need the Yak 28.
http://www.bobgear.com/trailers/yakdimensions.php
The last bullet on this page diffferentiates the regular Yak from the Yak 28, although it is far from clear. On my 700c wheels, I use a regular Yak with full SKS 50 mm fenders and 37 mm tires with no problem. I think there would be an issue with 29'er tires wider than 2 inches, but I'm not sure if these would even fit on the T2000.
Oops, you had a rack question. No problem. The Yak uses an extended skewer that takes the BOB fork well away from your rear triangle.