If you are worried about the exact order in which your PCB manufacturer applies layers, you would need to ask your manufacturer. It would be logical to print all the artwork layers before the solder paste but the only way to be 100% certain is to ask.
Same goes for the DRC violations: you always have the option of ignoring them but will need to tell your PCB manufacturer that this violation is intentional and should not be corrected. Otherwise, they might either reject your order, correct your "mistake" for you or possibly do something else.