I am a full-time LEO and own an upfitting business specializing in sale and installation of emergency vehicle equipment. I know a thing or two about this topic.
The reason your Setina partition has "flimsy" lexan upper side filler panels is because the cage was ordered for a side-curtain airbag car, which your's probably is. They are designed to give way in the event of an airbag deployment. That's also why the roll-bar has such a shallow angle from the door to the roof...to allow deployment room. The tradeoff is that the upper fillers are not as stout as the older 1/4" thick plexiglass fillers. Setina instructions call for the use of velcro to anchor the fillers while allowing them to break-away. It doesn't hold up. The solution to securing the upper fillers is to use a step-bit to drill two 1/4" holes through the filler into the upper-B-pillar trim. Then use 1/4" diameter trim fasteners (fir tree fasteners) to pin it down. This will work way better, be more secure, never come loose, and pop if needed in the event of an airbag deployment. If you do this when the cage is first installed, you can still use the velcro and then add the fir tree fasteners too for best results.
If you need new side fillers, I have a set for the Impala here, just IM me with your info and cover shipping. Or call Setina. Either way, DO NOT install a rigid substitute. The airbag could shatter a rigid plexiglass piece and send shrapnel your way.
For blocking your mesh window, a thin plexi sheet will work well. They used to be called hocker-stoppers. Put it on the prisoner side for easiest cleaning. Use 1/4x20 carriage bolts and large diameter (1.5" or so) fender washers and locknuts to secure it through the mesh. Make sure no sharp edges are facing the prisoner or you.