Actually, the Gov't does quite well with the negotiated rates - they are treated as full Y fares because thats what they are - at least as far as the airlines/gov't are concerned...
Your right the reimbursement paperwork is a mess... however that 30 day tickey you buy is nonrefundable/changeable... I travel for the gov for work a great deal, and have to maintain flexibility in my plans... if I need to change a day here or there the "city pair" ticket I have allows it... the full fare ticket that I sometimes have to (non contract rate)allows it too...
The real problem can be the room rate allowance.... especially in high cost areas.
Doomed to Coach