Well, you are certainly full of questions at the moment!
Okay, Togakure Ryu is taught as part of each of the X-Kans, however the way you may learn or study it will vary. Within the Jinenkan, the primary focus is to learn each of the schools as they are presented within the Densho, so yes you can learn Togakure Ryu (as well as Gyokko Ryu, Koto Ryu, Hontai Takagi Yoshin Ryu, Kukishin Ryu, Shinden Fudo Ryu, and Jinen Ryu [Manaka Sensei's creation]) as a separate system within the curriculuum. Manaka Sensei has created a series of VHS and DVD products of most of these systems, and that is where the youtube clip you are refering to are taken from.
Within the Bujinkan, Togakure Ryu is most often used as an influence to the overall strategies and principles, rarely taught separately. However, a number of instructors have taught Togakure Ryu specifically, whether at Tai Kai's, seminars, or just in the course of their general teaching, so it's not unheard of. And Togakure Ryu was a major part of the Bujinkan Training Theme for 2008 (from memory). There is also a VHS of Togakure Ryu from the early 90's, redone for DVD earlier this year, and they contain most of the scroll kata.
In the Genbukan, again it is part of the whole, but as you can learn individual ryu with permission from Tanemura Sensei, and he has begun teaching and ranking students in individual systems at Tai Kai's over the last few years. I think there was one for Togakure Ryu already, but maybe not. I haven't seen any Togakure Ryu products from the Genbukan yet (at least, not from Tanemura Sensei), but if they do bring something out, it will probably be just for Genbukan members, at least to begin with.
And finally, with regrd to the title of this thread, the Jinenkan tend to wear dark blue keikogi as their uniform. But if we are to look at a more realistic image, dark blue blends into dark environments better than black, so blue is probably a better choice.
