I would suggest using a non-breaking space (entered in as a tilde (~) inside Paratext) for your syllable boundaries. It’s already automatically replaced with a no-break space in the Preview View and would keep words from getting split by word-wrapping logic.
EDIT: Unfortunately, that doesn’t solve the Wordlist problem, though.
EDIT2: I tried adding the ‘~’ as word-medial punctuation in the language settings and, even though it showed a warning message about it, it seemed to make the Wordlist work correctly.