I would say no. If only 1 line is being used, then the excess air that is spread across the other 3 lines would end up being forced through the only open line. A caveat to this is if the pump has internal piping to avoid this situation and would just let the excess air out beneath the unit (for example).
I’d just recommend connecting the 3 closed lines to a single tube and then using that, or more ideally, downsizing the unit to just have the number of open ports you would need to use in your setup.