They can certainly be separated. The only reason they share the same pin currently is that the enclosure does not have a separate cutout for flow sensor. You can solder a wire from the circuit board and assign a separate pin to flow sensor, but most users are not going to be able to do so. In the future if we redesign the enclosure this will surely be included.
At the moment if you want to use separate pins, you can change the flow sensor pin definition in defines.h. You also need to make a few additional changes since a couple of controller variables are shared between the two (because the firmware assumes there is only one sensor). The changes shouldn’t be too hard to make. Just do a global search of OPTION_SENSOR_TYPE and you should find all places where the code handles rain sensor and flow sensor.