Silicone?...
I used the silicone after removing a mat from a Polaris 2 years ago. The silicone wasn't as strong as I had hoped. The girl I did the work for said she was sitting on it at the beach, nose pulled into the sand and it sunk down in the back. When I checked the mat, the edges were up a bit and some of the holes were open, allowing water to come in.
I think a stronger solution would be better. You can use any kind of plastic epoxy resinated material, like the JB weld type that you buy from the auto parts store.
If you use the silicone to patch with, make sure you use 3M-99 extra strong adhesive to put the new mats down with. This will keep the holes covered better.
Oh, and be ready because this stuff sets hard in a couple minutes. I used it on my boat and it stuck my mats solid within 10 minutes!:cheers: