Hey Phil,
The second profile I have posted are corporate type tracks, and those are completely royalty free as per my agreement with that retailer. They aren't allowed to be registered with any PROs. I also don't work with adrev or any of those DCMA type orgs that grab YouTube revenue based on copyright (I've noticed several royalty free authors using this loophole to get backend). That just seems a bit dirty.
The SoundCloud profile tracks, on the other hand, will depend on which libraries I end up working with and their policies. I believe those companies re-register the works under new titles, and walk licensors through the process of cue sheets, etc. But since I haven't worked with them yet, I can't tell you for sure. I'm sort of holding off registering any of that stuff until I see what's going on out there.
For bespoke stuff, it will be a case by case basis... I also do some work with commercial audio houses and they generally take care of the publishing like the boutique libraries, but sometimes it's a buy out.
It does appear that royalty free has become a lot more popular these days for the reasons you're mentioning... I can imagine this is a major time sink for indie productions.