Yes, this is often mentioned in Citi's marketing materials for the PremierPass and Chairman cards. The airline has no interest in incentives offered by your credit card company, and Citi has no interest in your frequent flyer program participation. They are completely unrelated.

However, it is essential to understand that Flight points are useless until matched by Purchase points. For example, if you use your card once to buy a 5,000 mile roundtrip for $400 you will receive 800 Thank You points (400 Purchase points plus 400 Flight points). The other 4,600 Flight points will remain pending until you make sufficient additional purchases to generate 4,600 Purchase points.