Simple comparison of silly gov't fares:
IAD-SEA: $600 (before taxes) (contract is with UA)
IAD-LAX-SEA: typically around $240-$260 (incl. taxes) (AA:IAD-LAX, AS:LAX-SEA)

The only issue I have is with the approved enroute time I can claim. Generally we get two hours waiting time at the departing terminal + normal flight time + airport to hotel. IAD-SEA = 2 + 5 + 1 = 8 so no problem with IAD-LAX-SEA being about 8 hours enroute. Shorter routes can pevent me from doing this. In those cases, I drive to DCA (yuck) and get the govt rate from there if AA has the city pair.

Our travel voucher system has a code to explain the reason for not using the contract carrier. My vouchers are regularly audited and I have never had a problem. The only issue I've ever had was one time failing to attach the checked luggage fee receipt to a voucher (from an AS flight).