MacBibble was one of the better .RAF developer apps for the Fuji S1 and S2 Pro, which had a weird way of taking the smaller-level, real sensor capture (3MP for the S1, 6MP for the S2), doubling it, working on it, and then saving the export JPEG or .TIF as either the "real" 3M or 6MP size; OR, taking the file and saving it DOUBLED, as a 6M or a 12MP sized image.
Not quite the same thing as X-trans, yet, more overhead, bigger files, more data, and more need to de-mosaic with good strategies. At the time,. ACR was very sub-standard. For a long time, Fuji's very own proprietary raw converter was the very, very best, but painfully slow.
As Ysarex mentions, RawTherapee was at one time, a pretty popular converter among Fujistas. I left Fuji before X-trans hit, but then picked up the Fuji S5 Pro, with its secondary highlight pixel options on the Expanded DR capture options. One of the weird things in my Fuji S1 and S2 experience was seeing the transition from "basic" RAW development, to the integration of "digitial fill light", clarity sliders, and highlight recovery to the raw decoding process: I spent the first five years without those concepts.
There's more than one way to approach image editing and RAW conversion, and different ideas on what needs to be done where, and when, within the so-called "pipeline". Hoep you can find a good solution for your current cam,S.