I always include "Manufacturing Notes" as one of the PCB layers
1) Before, when I didn't use it, always when I sent PCB into production I have got emails from PCB manufacturer with questions. It was very disturbing (I had to stop doing what I was doing and had to go back to the project) and it was also delaying projects (waiting for answers, sending emails between us). This was happening every single time when we sent PCB into production ... longer you work as a hardware design engineer, more your projects will be send to manufacture and if your documentation is not good, after some time everything what you do is just answering emails from your previous projects.
2) Since I include manufacturing notes, PCB manufacturers ask nothing. In case they asked for an information which can be included in the Manufacturing notes layer, I will add it there for the next project.
3) I do not normally specify holes tolerance. Normally PCB manufacturer uses numbers based on IPC specification or based on the machines they use. If you need to know it, try ask PCB manufacturer.
You can download our open source projects and see what we include in Manufacturing notes layer:
http://www.imx6rex.com/open-rex/