By 'HOTAS setup' you mean the section acessible from HARDWARE SETUP/INPUT/HOTAS CONTROL?
It seems to be exactly the same screen as that accessible by selecting simply CONTROL from the main menu as it doesn't do anything more than it. The scroll wheels dont work with any suitable "analogue" controls like pitch trim, throttle, rudder, aileron etc.
The scroll wheels can be set up to emulate M$ Intellimouse, ie. only one recognized.
I have an analogue throttle on my Logitech Interceptor and I can assign it (U axis) to a chosen input control in the HOTAS setup so it's not me doing something wrong. Too bad I can't use my old (and the best!) 'keyboard bypass' throttle unit with the Interceptor, the damn thing has a kind of digital data rely from the U axis and unfortunately the pots in the stick and the throttle are of different values so I cannot hotwire the stuff