if your box is made sturdy and its braced on the inside.. then the amp shouldnt be vibrating that much.. if youre getting something loud its conna rattle anyways if its close to the box. a lot of people mount to their boxes and dont have any problems..
btu abotu the plexiglass cover.. amps need to dissipate heat.. and if its covered the heat is just gonna saty around the amp and itll prolly go into protection early.. if you have to have plexiglass make sure its well vented