The method that FFDL (the standalone one, not the old FFF) seems to use is rather...expensive.
Basically, they open an invisible (
headless) browser and use that for Cloudflare bypass/scraping.
It works okay for FFDL because its GUI makes it clear that it's really only intended to download one fic at a time. But when you're checking/updating multiple fics at once, as FFF is intended for? it might be a bit more painful.