Thank you so much to everyone that has taken the time to reply! I really appreciate it!
So, I read the clasp nail thing too late and proceeded with the screw based solution. I did, however, buy a much better counterbore that perfectly matched my screws and also tried to minimize the hole and...
I've read that screws are better, I bought some decent floorboard screws and I'm finding that I have to countersink them a lot to get that 2mm-3mm clearance I'm after (the floor will need heavy sanding):
I feel like clasp nails are a better idea as I won't have to fill in these massive...