In my current typesetting project, the possible hyphenation points are determined primarily by syllable boundaries, not by hyphenatedWords.txt. Such points are most easily defined using a series of regex replacement rules.
I remember a few years ago seeing that it was possible to introduce soft hyphens uses changes.txt rules (as can also be done in Publishing Assistant), but in PTXprint, some additional settings were needed in the ptxprint-mods.tex file. But nothing I've tried has worked.
I see that under Hyphenation > Import List, there is a grayed-out option for "Add syllable-based hyphenated words", but I can find no documentation on how to enable and make use of that feature.