I believe your issue is that you shot using AutoDR (auto-dynamic-range) mode were the camera shoots a little darker or a lot darker to preserve highlights and then digitally brightens just the shadows by the same but variable amount it underexposed by when it produces its own JPGs. LR is showing you the actual underexposure the camera did without trying to compensate.
I think LR will artificially brighten DR shots that are done using one of the constant DR modes, like DR200 or DR400, but won’t try to compensate when each shot can be underexposed by a varying amount.
If you want to use Adobe products to process your Fuji photos, either turn off any DR modes or at least don’t use AutoDR.
Interestingly in your example side-by-side, I actually like the LR one better but I am assuming the suit was black but if it was gray then the LR one is darker than the subject looked in real life, but that is because the camera actually underexposed the shot.
If you didn’t have AutoDR set then something else might be going on, and it would be useful to have both the raw and the jpg originals to test with, which you can provide by uploading to somewhere like dropbox.com and posting a public share link to each in a message, here.
I think I did have the DR on Auto which would make sense, but it should be carried over to Lightroom/RAW which is annoying. This comparison wasn't a very good one to pick since it was outside but all the ones indoors were way underexposed after the import and I have to correct everyone by upping the exposure and shadows. Not a huge deal since I can just do them in batches but a pain.
Here a good example, taken with low lighting at F1.4 the top one is the RAW file with DR Auto. Second photo is after its been imported. Its a shame that the in camera processes dont get carried over to Adobes editing programs. I guess Ill try some other ones such as Capture One and see if it does the same thing. Ill keep DR Auto off next time around. It also seems like the photos are a lot softer as well, hopefully Adobe makes Lightroom more friendly to Fujis RAF files.
Adobe usually ignores all camera settings other than WB and crop-factor so they are doing extra just to get DR200 and DR400 to work. On my Canon DSLR if I have highlight-tone-priority turned on, which is similar to Auto-DR on the Fuji, I get dark images.
I will never get a Fuji with the X-trans sensor, because Adobe’s processing isn’t optimized for it.
With how popular the Fuji cameras are becoming they should probably work on allowing Lightroom and RAW to use those settings. I think for this shoot ill edit in a different program and then turn off Auto DR for future shoots until they fix it. Thanks for the help in figuring out what it was doing.
From Adobe's point-of-view there's nothing to fix, I don't think.