Matt
This has been dealt with several times within the X-T2 thread, and even today I posted a load of information about processing Fuji RAWs
In essence though, before the X-Pro2 was released, first X-Trans3 sensor, Fuji worked with Adobe to get better results, this has resulted in different Lightroom processing being required for X-Trans3 against the earlier versions.
Adobe have continued to improve X-Trans processing ( 1 and 2 ), but many prefer other options for these sensors.
Personally I've not noticed a difference between the latest CC and the previous version.