I haven't actually bought it and used it a bunch yet, but I did a two week trial of NCPlot, which was at least fairly accurate. You can put in your work coordiantes, so travelling between fixture stations and how far to tool change position can be accounted for. It could also handle sub programs. It seemed pretty neat, and I liked it. I'll probably pick it up at some point. It was nice having something to give accurate cycle times so I could play around with different things on a part that is running to try and speed things up. Having an accurate simulator would make it a lot easier to justify buying better tooling for a job or not.
I think no matter what the software is though M codes are going to affect somewhat the cycle time differences between computer and machine. How long fot the spindle to ramp up/stop, B axis clamp/unclamp/, etc. But, yes, an accurate time of machine movements would be nice. Peck drilling definitely affects the cycle time calculations a bit between CAM and reality. Also in MCAM, I don't know if they fixed it yet, but in X7 still the helical boring times are always shown at half of what they are actually.
Doesn't answer the simultion part of your question, but I will go a little OT and say for jobs with lots of drilling - Why don't you have HP drills that don't need to peck in the machine? Good drills are one of the easiest ways to speed up machining a part.
And for quoting purposes, the way I approach it matters a lot on quantity. Big volume needs an accurate cycle time estimation, tooling costs, etc. Onesey twosey...not so much. A guy told me years ago when quoting the onesey twosey "You know how to machine. Just look at the print and ask yourself 'How long it will me to make it?' Write the number down and move on."