I'm not sure if this was brought up already...
From the top, when drilling, apply masking tape to the hole and the area around it...
Keeps the scratches from the shards of hot sharp metal from the hole popping up and scratching your paint... Also tends to save you if you do make a mistake and slip...
Always drill a pilot hole first (uber small) to verify clearance on the other side... Makes drilling with a hole saw a bit easier
Use a deburring tool on the edges of the hole to ensure a good mechanical connection that isn't going to cut your fingers off when you try routing the mount thru the hole.
Typically we do sratch away the undersurface part of the sheet metal for a good binding contact, however, we run primer on the edges of the sheet metal of the hole to prevent rust if the seal on the NMO fails. On industrial applications (i.e. trucks going to Canada), we also spray everything down with primer on the underside to keep rust from occurring where the paint was scraped off for the under contact. This is AFTER tightening up the NMO mount.
Bravo for taking the jump and getting away from mag mounts!