Charlie, I've been using silicon in my work shop for forty years. Of course, I don't get wild with it, spraying it everywhere. But then, I don't smear wax all over, or spray other "slickeners" all over either.
I have a shelf of all sorts of magic lubricants, which includes Teflon, a Teflon mix, silicone, grease, oil and so forth. The Teflon type and silicone type get used on pipe clamps, lock down knobs and so forth.
I keep only the oil free type around, since I have better luck with it for what I use it for. Not having oil in it helps, since the oil wont let go of fine dust and just contributes to problems on down the road.
Spraying silicon on gears under the table shouldn't affect anything on the table.
On a couple occasions, I even flooded the table top with it. It helped float light rust off. Of course, after I was done, I wiped the table down - very well.
If I sprayed more, I might have to be more cautious in my use of silicone, but a little common sense in its use seems to go a long way.
Most my finishes get a penetrating coat, then a brush finish and, if needed, a buff and polish. Others get a thin coat of shellac and some even get a thin coat of Elmer's white glue. When I'm in a hurry or otherwise need it, I spray. I don't remember a single fish eye.
I'd have to lay the silicone on very heavy, almost intentionally, to get it to stop a penetrating finish, since it doesn't build and fill the pores. After the penetrating coats hardened, future coats would be adhering to it, instead of the raw wood.
This is not to say your concerns should be abandoned, because I've seen what silicone does to automotive paint finishes (and which can be overcome, but with much more work). I'm just saying be careful. For example, you can let it set to penetrate microscopic pores of cast iron, but you should get rid of all excess.
If you have to, steal another of the wife's shirts to make sure you get it all off, but use her cotton ones, since they seem to work better. :laugh: