Answer from a guy who knows not much about TMNT:
IDW and Dark Horse might not be the best of buddies at the moment, due to much noice regarding the Angel license.
Things might have lightened up a bit now, but they weren't for a while ago.
(Short story: Dark Horse had Buffy and IDW had Angel. Later on, Buffy's big bad in Season 8 comics, Twilight, turns out to be Angel (done within the rights of the license, but still..)
and Joss pushes on for Dark Horse to get back the Angel license. Which they get. And a lot of the press was very poorly handled by Dark Horse.
Example: the news of getting the Angel license back comes in the letter column of a Buffy comic, NOT in a joint press release from both parties.)
For full disclosure: YES, I'm a disgruntled Angelfan..
BUT, Usagi Yojimbo is creator owned, so it's up to the owner Stan Sakai (right name ?), what he wants to do.