To be honest, I'm not sure how it worked - everything on the booking was under the alias name, but I used my passport when going through security etc. I assume the company dealt directly with the airline, and there would be a flag in the system that security and gate personnel would understand

I was in the IT security side of things when I worked for them, so that's why they had me travel under an alias - knew vulnerabilities in their network etc - never actually did any transportation myself.