Microcontroller is designed exactly to do that: control the IO the way you need. For example, if you need a deadtime for break-before-make operation, just turn the GPIO bits on/off in your desired order, with a small delay inbetween. But for this to be easy and straightforward, you need separate IOs.
Is it really possible you are out of IO on such a large device, and need to save one pin by combining the control of two switches to one IO?
We need more info.