In essence you are going to create a gasket. I would try it out first on a small piece (not your tank lid).

You put the silicone down on one side and let it set-up a bit. You compress it (with your screw-down); however, don't go all the way down. You want to then let it cure and THEN you compress it the final amount.

The other option is to simply GLASS IN THE BOTTOM with and appropriate fiberglass finish. (Seal all other sides of the plywood with epoxy) Then seal it as you planned.

Gene, check the web and I think you'll see that Silicone won't adhere to PVC; and, you should be careful with other sealants and drinking water. I think the silicone COULD work, but it will essentially be a gasket on one surface. You need to make sure it really can function as a gasket. I'd seal all the exposed wood with epoxy down there, just in case.