It's a matter of perspective. I think I've been on a boat that had inspection ports in the seat back, but the owner had mounted oarlocks, so I'm thinking those were placed further back.
A hole in the bulkhead lets you view the entire repair area side on and without mirrors. A hole in the side allows you to reach in more directly. I can see both of them having advantages.
I also remember reading that there can be a "stringer" or reinforced section in the seat back other than just the backing plate under the track. (Unless said poster confused the backing plate for some reason).
A 1-2" hole in the bulkhead could be used to get a good look at what's underneath the coaming (and given the location is easily patched w/o the need for an inspection port). This could help verify the intended placement of the access as well as assist in evaluating the conditions.
With all the nifty gear that's out there, could also be used to light the area and give a live view of the repair. Just thinking out loud here.
Or, you could just drill where you are planning to and I'm sure you'll manage. (I' can't promise you it'll come out alright, that's up to you

).
PS: when doing any fiberglassing: make sure to do the layup (all layers) in one piece on a strip of plastic and transfer it in place with that backing like you would a piece of tape. You can abandon the backing in place, or pull it off when the epoxy has cured. It strikes me that some kind of "balloon" would make a good support for the repair while it's curing.
However, you might also decide to just epoxy seal a strip of wood for the new backing plate, perhaps with a single layer of glass and let that cure outside before gluing it in place. (Sealing has to cover all 6 sides and all holes have to be sealed as well). But you knew that.
Could be that access through the cuddy makes it easier to slide in a single piece of wood and that's why people did it that way? Anyway, any glass over the backing plate was an attempt to seal it / hold it in place and not so much intended to strengthen, that's my take.