I've had cory cats and kuhli loaches on flourite before, and it didn't seem to be a problem. Also, lots of people on here keep cories on blasting grit, which is likely more abrasive/sharper then flourite.
I'm not sure there is a good reason to do this, unless you just like the look of pool filter sand. Plus, if you are using PFS as a cap, you may as well use something like dirt, or oildri or safetsorb underneath, all of which would be far cheaper then flourite/ecocomplete and may even work better (nutrients from dirt, better CEC for oildri/safetsorb).
As to separating the layers, I'd go with something similar to what steven p said. maybe get some cheap polyester batting at a craft store or something.
Or a coconut coir type basket/pot liner - sometimes you can find those pretty thin, it would allow roots to penetrate, and it would break down over time (on the scale of years), so it shouldn't really restrict plants or anything.