Thanks for the heads up on the holes. I got the cap from the manufacturer (X-Yachts) and it wasn't just the screw on cover, but the whole thing - the cap and the deck mounting. I haven't yet taken the old one off to see if the screw holes match, though I imagine they will seeing as how it's an original part...
It's monsoon season here in Singapore and I'm waiting for a dry day to change over to the new part - I imagine silicone or 3M 4200 will prefer a dry environment to be applied.
Thank you again for the kind advice.