Is Bujinkan heavy on small joint manipulation?Actually, no he didn't. He just said it messes with some techniques. And that's true of a lot of traditinoal small-joint manipulation. Most of them can still be done, but are either harder to get to or are easier to resist when wearing MMA gloves. Larger gloves make many of them impossible.
This is not a factor for systems that don't train much on small-joint manipulation (like Judo, for instance).
I don't know. I do know that I've seen plenty of YouTube videos of Bujinkan practitioners sparring with other martials artists - I've seen Bujiunkan versus karate, judo, Muay Thai, BJJ, and MMA - and Bujinkan appears to be primarily a striking art. In fact, I can't recall any instances of Bujinkan guys even trying to grapple - not even against other grappling arts.
I'm open to the possibility that there are some nuances that I may have missed.
In life in general - not just martial arts - when someone focuses on why something won't work, rather than trying to find ways to make it work, what they say becomes that much more dubious.