Weatherproofing isn't a problem. The grommets are good for chafe guard. Just coat the wire and grommet with a marine sealant for additional protection.
I'd be a bit concerned about passing autopilot wires thru the pedestal if they're anywhere near your compass. As you know, any current passing thru a wire creates an electromagnetic field around the wire; the strength of that field -- and the potential for mischief -- depends on several factors. You might run a test...if that's practical...before finalizing the installation.