Doing that would require a complete redesign rather than a modification. Moreover, a fan on top wouldn’t work all too great since there are hot parts on either side of the PCB (the SoC and an optional modem on one, the Wi-Fi board and an optional SSD on the other). Still, there are 3D-printed case projects exactly like you described published on this forum.
Just received my BPI-R4-Pro board… in case you might need a guinea pig… 
Sure, although I likely won’t have the time to work on the Pro case until earlier next year.