I'm not sure you understand what I'm getting at ...or maybe I'm just overthinking this:
While the fasteners provide great clamping force, such clamping force alone might not be sufficient to prevent shifting/slippage over time. Alignment pins would help prevent any such shifting/slippage, and thereby preserve long-term shear load capability, in a way that threaded fasteners alone cannot - presuming the use of fully threaded bolts. While carefully selected partial-thread bolts (sized to snugly fit the mounting holes of both the Plexiglass and enclosure panels) would provide both positive alignment (to preserve shear force resistance) and clamping force (and, as such, might well be the most elegant solution), a fewer number of alignment pins (for example, four alignment pins, versus twice as many - or more - alignment bolts) might be a lot simpler to implement.