Marking and cutting the hole...
One way to look at the cajon is as a Helmholtz resonator. Not sure how accurate that is, really, since the volume of air in the cajon isn't doing to much resonating, but assuming that the air spring's oscillation after a strike influences the kick sound, one might infer that the size of the hole would affect the "pitch" of the kick. The original plan was to keep the disc cut for the hole and use it as an adjustable slider that could narrow or widen the hole. Testing it out, it seemed largely irrelevant. One might then infer that the size of the hole doesn't matter so much. Even so, intuition tells me for some reason that perhaps this hole was a little too big (it was scaled up a bit because of the general oversized nature of this cajon.) The exit hole for bass reflex ports is often shaped in certain ways. It may be worth experimenting with those ideas. It's also tempting to wonder if the internal reverberance of the cajon maximizes the energy delivered from the tapa: perhaps the frequency is low enough that it doesn't matter, but perhaps some shaping of the cajon or strategic insertion of wood inside would help keep those waves coincident (in-phase). One wonders too how the location of the hole affects this, if at all.
The hole on this cajon is on the side, close to the floor. A cajon has the most punch when played against a wall, or especially in a corner. This leverages the bass effect: when placing subwoofers or a bass amp in a room people often choose corners or, failing that, against walls, because bass frequency waves, with their long wavelengths, are less susceptible to canceling each other out when reflected off of nearby surfaces and redirected in a similar direction. Thus one can "collect" the energy emanating from the cajon in all directions, bounce it out of a corner, and focus it into the room as a unified force. If played in the middle of the room, the waves go everywhere, and their reflections of walls may intersect out of phase, thus reducing the bass sound dramatically.
Thus, one sees the wisdom of having the hole in the upper back: you can play against a wall or a corner. When you get up against the wall and tilt back on the cajon (a common playing style) the hole is right where it should be. There may be advantages to having the hole in the side; I wondered if it somehow improved the bass by forcing the internal aerodynamics to a lower resonant pitch. Perhaps it is easier to mic on stage because a player tilting forward and back can't accidentally change the distance to the hole from the mic (nearly as much, anyway). But having the hole on the side makes it difficult to find an appropriate place to sit to maximize the bass sound: you're always facing along the wall unless you're lucky enough to find a corner (harder than you think).