Silicone lubricant is certainly a problem for wood finishing or painting, but I doubt that cured silicone caulk would be a problem. It will initially have some acetic acid in it, but that'll go away when it's cured. You can buy stuff that is safe for food contact, and so I'm not sure how it could harm a print.
You could also use little dabs of epoxy, assuming it will stick to the plastic dividers.
Another option would be to put window screening in the slots. Use two sheets. You might have to use stainless steel clips to hold the top two corners. (I use clips from Radio Shack test leads to dry my negatives on a line. I've used them for years, and they haven't rusted, nor have they ever dropped a negative.) Put the print between the sheets.
Another option would be to wind heavy fishing line around the plastic sheets.
Anyway, you could always do what I did: make a new insert. I used stainless steel bar, ss threaded rod, acrylic tube, rigid acrylic strips and fishing line to make a 4x5 film washing insert for my Versalab. It's not hard, but it is a little tedious to make such a thing. But you only have to do it once.
All that said, I've had my Versalab washer for about a decade. I tone all of my prints in selenium and sulphide, just enough sulfide to give added permanence, and I've not had any problems with too much fixer being in the prints. (It true that a problem could show up way down the line.) When I got the washer, I did run some fixer tests, and I didn't have any problems. I do use a wash aid, and all of my FB prints wash for at least an hour after toning.