FWIW, coming from someone who doesn’t have a camera using the new style Fujifilm batteries… (Which arguably haven’t been around long enough for battery problems to become prevalent anyhow).
I’ve had good luck with Wasabi brand batteries in my Fujifilm, Olympus, and Panasonic cameras. I generally start any shooting day/session with a fresh battery and the battery removed from the camera is topped off regardless of its charge state. I don't intentionally run batteries down to empty — though it does happen.
I primarily use an external Nitecore charger, though I will charge a battery in-camera under certain circumstances. For example, if I’m traveling very light, or to top off an in-camera battery during a break, or prior to my heading out the door (if a battery swap isn't expedient). I avoid leaving a charger connected to the camera for long periods and I monitor all batteries, Fuji and third-party, for signs of swelling. (So far none found.) Using the inexpensive Wasabi batteries allows me to rotate through a relatively large library of batteries for each camera. No single battery is exposed to multiple charge/discharge cycles in short order on a regular basis.