It all depends upon how close your bolt handle fits to the front of the bolt cutout before and after the action is trued. The closer it fits to the front of the bolt handle cutout in the receiver, the more extraction camming you will have. I've seen new Remington's that were marginal on the amount of extraction camming that they had, caused by the bolt handle being placed too far rearward when the bolt handle was attached originally. If you take one of these that is marginal originally and then remove metal from the bolt lugs and the receiver lugs, it's going to make the amount of extraction camming worse.
As to removing all the color from when you checked lug engagement, if you have the firing pin assembly and have a trigger in the action, the trigger will push the rear of the bolt up. The top lug will not be engaged until the rifle fires. The rear of the bolt will drop and the top lug will come in contact with the top lug in the receiver. The only way that you can check for lug engagement with dykem or a marker is with the firing pin assembly out of the bolt.