In Genbukan we are indeed able to learn specific ryuha.
first of all, elements of specific ryuha are identifiable in the Genbukan and KJJR curriculum. What we learn comes directly from the ryuha in many cases. Then there are the 1st dan requirements, which are specific kata from specific ryuha. IIRC 3 times 6 kata (from 3 named ryuha) with their ura and omote variants.
After BB, we're allowed to receive licensing in specific ryuha as well. So I can work my way from Shoden, to Kaiden and receive the transmission. There are various requirements for being allowed, and this is beyond the scope of this discussion.
I think it is fair to say that schooling in the general GBK and KJJR curriculum is not the same as learning a koryu art. Even though the training methods are fairly similar to koryu, the reality is just that as a whole, it is just different from the way that things go when you actually join a koryu. Koryu transmission teaches specific concepts. The general curriculum does not do that. We learn the techniques, and our concepts are a mash of the concepts, the way Soke wants us to learn them, which is his own interpretation. And of course, we do not have the cultural content of a koryu.
Even when we receive licensing in a ryuha, we can argue about whether that consists koryu transmission or not. By the time we'll get to menkyo kaiden (which in my case will be ... probably never) we'll have received a full transmission of the system, including kuden. So from that pov the transmission is legit.
However, for the people not living in Japan, most of the transmission of the ryuha is done in (BB) seminars on taikai where also the testing is done, via dvd (for preparing for the taikai) and is built on top of the basics which were learned as part of the general curriculum. So while the content of the ryuha was transmitted whole, it was done in a manner that is not the way things are done in other koryu systems. This is of course a matter of opinion. I could see arguments either way. In the end, the most important thing is that the lines continue and that the system survives.