The purpose of splitting the lists into folders is to make recording and otoing more manageable processes for the general UTAU user. Since the tutorial series encourages use of OREMO, it's fairly simple to just record multipitch using the existing folders by putting a suffix on the filenames themselves. There's a separate "typelist.txt" in the OREMO files with arrows for a high/low pitch, but it can be customized with note names or append letters/kanji.
I'm assuming that at this time, the currently released reclist contains all recordings necessary for a basic American English bank. Chezzie mentioned a future simplified version for non-English speakers, which will presumably remove some samples.
Oniko's multipitch method is actually quite prone to FRQ errors, a concern that Myst mentioned when working on Aiko's multipitch CVVC. Also, the recording method intended for VCCV™ takes advantage of using specific timing according to a BGM, so that the base oto easily fits. If you want to go through the effort of ignoring the BGM entirely, duplicating oto entries by hand to create more aliases and base values, then recalculating the consonant velocity adjustments required for the approximate speed of the actual recordings, go ahead.