I'm an amateur/hobbyist (but relatively knowledgeable as I work in the film business and it's partly my job to understand photography) who shot Nikon and then Canon DSLRs from 2009 to 2020, when I bought an X100V out of curiosity.
-- To me, the single hardest thing in making the switch was understanding how the "concept" of the camera, and especially custom settings, had changed. Back in the old days, the custom settings related to how you actually used the camera. For instance, sometimes you shot still lifes, so you had certain focus settings for still lifes. Sometimes you shot sports, so you had completely different focus settings for sports. You could save different "banks" of custom settings for those things and switch between them with one knob, as you probably know.
-- The Fuji had me confused about this for quite a long time, as I didn't understand why I couldn't save certain focus settings as part of a custom set-up I would use for still lifes, or sports.
-- Slowly it dawned on me that the Fuji is really about manipulating jpegs IN CAMERA and the concept of the custom settings really has to do with the idea that each "bank" of custom settings creates a certain look, rather than a "way" of using the camera depending on the subject and whether it's moving, whether it's far away, whether it's night and you need really high ISO, etc. Once I understood that, I found I stopped being frustrated with the settings and understood what they are for and what you can do with them.
-- So, to respond specifically to your point, I think this new Fuji "concept" is what's really behind your frustration. You can't save focus settings as part of a custom settings bank, because the "concept" here is that custom settings are for image quality stuff like image size, film simulation, grain size, etc etc.
-- Lastly, I hope I'm right about this, and I hope it's helpful!