The system should be (or allows alternative settings) from Vocabulary readings (or audio or EN) + radicals => Kanji => Kanji compounds.
Apparently, Vocabulary readings (or audio or EN) can be done in self-study script, but I don’t think native WaniKani has this feature yet.
Nonetheless, studying Anki exports in advance can help with this. (Not sure if some created an audio-based WaniKani deck yet? Might be the best way.)
EDIT: Vocabulary reading, rather than Usually-Kana vocabularies. I don’t know if WaniKani team would agree, but I like learning Jukugo before Kanji itself (actually Kanji non-seriously pre, and seriously post).
Also, lone Kanji with long readings and perhaps Okurigana can be learnt without regards to Kanji at all. (I am always against learning Kun reading and clipped out Okurigana.)