i could throw a monkey into the wrench.
If you put a piece of plexi on the bottom, you could bond the plexi together into one big peice. All plexi glass "glue/cement" is, is just ground up plexi glass and a solvent. So when you apply it it slightly melts your plexi, then the solvent disapates and you are left with a joint made of 100% plexiglass.
If you still want to do what you are going to do, there are 2 ways. If you want it real strong, use a router (or circular saw if you dont mine a through and through cut look) to make some 1/4" deep channels for the plexi to lock into. Then bond them to the wood using PL400. You can pretty up the joints with a rubber glove and some rubbing alcohol. Your other choice is to use the PL400 without the channels, and just big fillets.
But RTV is not a bonding agent nor adhesive, its a sealer/gap filler. It doesnt have any "strength".