I don't have the Steam version and I know it only like you describe it but with my X52 Pro.
When I launch my joystick calibration tools I see that some of the wheel knobs on the throttle controller change constantly somewhere in the 0.00xx range. It's not much but it seems to be enough for X4 to consider "Joystick Mode". After all this didn't happen with my old joystick that had only X and Y axes and no other rotary buttons.
Seems like configuring a deadzone in-game has no effect on the rotary buttons.
So my solution was to solder a salvaged on/off switch into the USB cable (see https://beko.famkos.net/2021/05/20/335356/ for picture). Problem solved. I wasn't happy with USB draining power all the time anyway
I'm aware that such usb interruptors can be purchased but I wanted to play and was furious already