The game will turn out to use a single sequence file, the one you talking about, for all map themes. The game dynamically mutes different instruments on the song to produce different variations. There is currently no support for a feature like this with 2SF files, which is why there's no such thing as a nice clean Metroid Prime: Hunters or Mario vs Donkey Kong 2 set.
*opens eyes*
It sounds too terrible to be true....but these premonitions have never been wrong before!
Actually, it is possible to create rips like this. However, it's not really that easy, and those who are capable of doing the necessary modifications are few and far between. One of them passed away recently. Although ugetab might have had little or no experience with 2SFs (I don't know one way or the other), he ripped a lot of dynamic USFs. Some of them involved "simply" hex-editing the USFs to mute the appropriate channels. Others required complete re-rips. I suspect that the Yoshi 2SFs you're talking about could be recreated via hex-editing the 2SFs (or 2sfLIB), but I have no idea what section of the files would need to be altered for that to work.
Sorry "we" (in general) can't be of help here, but at least you've got a rough idea of what the problem is. Mouser X over and out.