As far as I'm concerned, they might as well put Bayer sensors in all bodies.
I don't believe there's much IQ difference either way. When they just started Xtrans, they offered less moiré, with the downside of muddy or crunchy fine details in certain color ranges (muddy skin tones, crumchy grass). As time went on, Fuji and several raw developer software both improved the demosaicing to reduce the muddy / crunchy details. At the same time, Bayer sensor manufacturers used the general trend towards higher res sensors to reduce moiré despite removing anti aliasing filters, which reduced the downside of and Bayer. Hence as of 2020, I don't believe there's a significant IQ difference either way.
However, Bayer simply plays nicer with more raw developers, so that pleads in favor of Bayer. And Fuji knows how to get amazing jpegs out of Bayer sensors, just look at the original X100, which many still rate as the most pleasing jpegs of the X100 series. So Fuji doesn't need Xtrans to get good jpegs.
I believe right now Xtrans has more marketing benefit - dare to be different - than IQ benefit, hence they will probably keep using it on their higher end non-medium format models (funny side note: the GFX 100S, with its Bayer sensor, has almost exactly the same size pixels as the XT3).