If I use non-government funds to pay for flight on non-U.S. carrier, can I then use government funds for other costs of that trip? The Fly America Act states that all U.S.-government funded travel must be done via U.S. air carrier service (there are some exceptions, but none of them apply to my scenario).  I recently received a travel grant from my university, independent of any government research funds, and I know that I am allowed to fly non-U.S. carriers with that university travel grant money.  However, the grant does not cover all of my expenses for this trip, and I wanted to use government funds to cover the remaining.

Can I fly on non-U.S. carriers and pay for the flight portion of the travel costs using the university travel grant?  Would there be any issues with this?  To reiterate, I would only use the government research funds to cover non-flight portions of the travel.
The text of the Federal Travel Regulations explicitly states:


  You are required by 49 U.S.C. 40118, commonly referred
  to as the “Fly America Act,” to use U.S. flag air carrier service for all air travel funded by the U.S. Government, except as provided in §§301-10.136 and 301-10.137 or when one of the following exceptions applies:
  
  [...]
  
  (g) When the costs of transportation are reimbursed in full by a third party, such as a foreign government, international agency, or other organization.


In this case, since you are not requesting federal funding for your air travel, you can use a non-foreign carrier. Clearly, foreign travel will most likely require lodging and per diem costs at non-US-owned venues—unless you happen to like staying at Holiday Inns and eating at McDonald's, Starbucks, or Pizza Hut. Moreover, the above portion of the regulations say that if improper air carriers are used, only the transportation costs are ruled unallowable. It does not talk about the per diem expenses for lodging, meals, and incidentals.