well i think the rank of the unit plus the custom skill preset in mod folder doesnt actually engage because i made it so privates were completely hopeless whilst the max rank was like tier one operator and the privates beat them occasionally and both seemed to lack on distinct draw backs or merits as dictated by their skill. I would say have preset customised to your liking like maybe the top 3 ranks that arent traditionally used in a 3den editor squad composition to have ur custom set up. however im not sure how one gets the skills predesignated on the config file to engage because i just select the rank for each unit and it doesnt work and i tried copy and pasting the config in to their init and it still didnt work so im not sure if its a bug or we are both missing something key. so i havent done anything to disable the rank=skill presets but regardless of rank i see little change in skill so maybe your not actually looking at ur ai vcom skill ranks but ur difficulty rank settings could be the main influencer. i have been trying to fix this for the last month but i still get colonels loosing to privates and stuff like that and both being equally hopeless at killing one another. i hope this helps, i know our problems arent the same but ive been playing around in the same field you have.

As server host, make sure file patching is enabled. You can select this in the Arma 3 Launcher under Parameters -> All parameters :)
Otherwise, the userconfig will not overwrite the mod config. You can see if it is working succesfully by turning debug on in the userconfig and then running a mission - there will be text notification for men down, radio calls, etc :)