I was thinking if i went the exo terra route of having the bottom of the tank drilled so i can use a sump tank like they use with a Reef setup.

The setup with a drilled tank would be pretty simple, Hole in the bottom of the tank with a sink plug fitting. Short tube out of the bottom of that with a sock of fine material to catch debris. All into a smaller slave tank with a high pressure pump in it.

Back in the main tank you would have to raise the Substrate on a fine mesh with a frame. Other than that you would be free to invent the interior without the need to make allowances for pumps.

As for the plastic divide idea I've done a few now. They work very very well, But make sure you use the correct silicone, and if your holding a large volume of water back then brace it correctly. To remove a plastic divide done in this way you twist the divide out then cut the silicone off the glass with a scalpel or stanley knife blade. The only hard part is getting silicone off the other silicone, but in most cases it should just pull away if your gentle. A word of warning, Cut the corners on the plastic divide so they avoid the tanks silicone seal all together, then Back fillt he hole with a good thickness bead of silicone. If you cut away at the tank silicone thinking you need them corners to be tight you may end up with a leaking tank!!!