In this photo I still need to countersink the flange side of the bolt holes slightly. The reason you want to do this is to create an o-ring like effect of marine bedding compound surrounding the threads. If you don't countersink most of the sealant will squeeze out when you tighten everything down leaving very little to prevent a leak. The premise and design is that water should never even get to the top side of the backing plate but just in case it's best to countersink slightly and make and create an o-ring effect.
Countersinking any hole, where marine bedding compound is to be used, is a good idea especially with deck hardware. This slight countersinking makes a nice water tight gasket and also prevents crazing of the gelcoat from the sharp and abrupt edges a straight drilled hole creates!