What's the root cause of water getting into the tire well? Until you address that, any other remediation is a band-aid that won't work long term.
Fluid film almost certainly won't attack the rubber on your tires. Just think about the implications if tires were attacked by other, lighter hydrocarbons? If a spill at a gas station led to tires dissolving? No, they've thought of this. The warning on Fluid Film is more likely for things like butyl rubber sealants, which aren't crosslinked like your tires.
But Fluid Film is messy. I wouldn't want it in my tire well. And silicone is a poor idea. It gets everywhere, interferes with adhesion of anything you'd like to stick to anything (like paint), and it's not going to protect from moisture. Don't go that route.
My recommendation would be (1) fix the source of the water getting in (or not getting out) and (2) paint the well with POR-15. It's kind of a pain to use, but it's simply *perfect* at things like this.