I go by my middle name, and 3-4 years ago, when someone else at the company used to book my travel, they put my middle name on the ticket several times before I managed to correct the behavior.

I had to explain it to the TSA agent every time, but I only got seriously harassed by it once, and even then made it through eventually. (The agent sent me back to the airline to change it, then they said no and sent me back to the agent, who relented.) Most times though the simple explanation did the trick. My middle name is after all printed on my driver's license so it wasn't so far fetched.

As for miles, I _think_ I recall still getting miles for those flights still booked under my middle name, but it was years ago and frankly at the time might not have been paying attention as much as I do now, so from this perspective my data is probably not good.