Well, the system you describe sounds like it's wide open for abuse, because someone can run out and survey airlines to find the highest possible fare and then use that as a basis for comparison.

The usual method I've ever seen/heard of is that the corp. travel dep't will price out an itin. for you using the preferred carrier. If you can find an alternative way of getting there for less than the preferred carrier (another carrier, different return date, etc..), the company will split the difference with you. That's a win-win.