Hi, best practice when mounting/bedding deck hardware on a cored deck is to remove some of the core surrounding the holes to protect the remaining core from water intrusion.
For big holes, traditional tools can perform this job. For tiny holes, like one for a single fastener, a person can apparently use a bent nail in a drill.
For medium sized holes, like for cockpit and deck drains, I found that I could not get regular tools in there, and a bent nail would just jump around as it made and lost contact with the core. Maybe a sturdy hand and drill press guide or attachment could make this work. But after trying a few grinding bits for my drill and Fein MM, I tried a Kutzall Extreme - Rotor Saw Burrs (RSX-114F) in my drill. It was easier to control, worked fast, and appears to me to be an ideal and inexpensive solution for this task. I'm not sure where they are sold, but I got mine on eBay:
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