Yeah, I've considered hiding mine under the seat like that. My only hesitation, is that my cafe project had one requirement. The ability with not too much work to swap my solo seat back to the stock two person seat so my wife can ride with. If I hid the battery under the seat like that, I'd have to move the battery back to stock location when the 2 person seat is needed. Seeing that I will likely not ride with a passenger but 1 to 2 times a year, moving the battery wouldn't be too much of a pain if needed.
I've got the same problem with my cafe project. my plan is to take the stock battery holder and resize it or cut it down to fit the PC 680 exactly. than get rid of the plastic battery box side covers and sheet metal the sides in.... Like below: