be aware of colours
If you paint it black, light no longer passes thru, thus the plexi must ABSORB all the light energy.... this will heat it and cause local expansion....vs very little on the clear area adjacent, introducing stress. No problem if your holes and edges are smoothed perfectly, but how do you know?
.......just a cautionary note.
if you paint the inside, the colour will be different due to the tint of the plexi, and the reflected light off the surface.
If you can match your paint colour, you could apply vinyl graphic sheeting to the area instead. (Not likely as permanent...a pro & con!)
I'd steer away from chemical bonding agents, when mechanical abrasion is possible/preferable.
Google the tech data for painting plexiglass, and you'll see some good recommendations.