As is these are quite confusing, since they don't say LiquidThreads, just things like "Threaded discussion" or "Email me on replies to a thread I am watching" so are likely to be misattributed to Flow.
This can be done with $wgHiddenPrefs . They are:
lqtnotifytalk, lqt-watch-threads, lqtdisplaydepth, lqtdisplaycount.