You should talk to your board house and discuss with them what data they need and what you can deliver for countersunk holes.
If they get a separate drawing, they have to digitize it and edit the needed NC drill files manually, but this takes time and money.
A Gerber file is data for photoplotters, but not for NC drill machines. The board house may transform a Gerber file into the needed NC drill file, but this is a manual process using their CAM CAD system and will take some time again.
A separate NC drill file for the countersunk holes only will be the best data for them, but you should discuss the details with them.
But you should be aware that countersunk holes will require additional drill jobs for the PCB, especially if both sides are countersunked. Drilling two or three boards together in a stack as usual is not possible for the countersunks, each board must be drilled separately. If you want to reduce costs, try to avoid countersunks if possible.