I just use a bit of sikaflex to seal the hole. I leave a few threads clean so I can just screw in the bolt if the anchor points need to be used. After the deep river crossings a few years ago, when I had to lift the carpet, I found a more holes than I could poke a stick at. I spent a long time sealing them and the edges of all the plastic screw inserts.
I even glued some rubber discs over the holes in the top of the sill panels and up the pillars. I also used some small food containers as junction boxes to seal off the loom plugs under the front passenger seat and also the wiring and relays used on the air compressor under the rear passenger seat.
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