Tour/Cruise Provider Air Fare

Are Tour Companies given incentives to book less popular flights?

I have seen several occasions where a person getting Air through the Tour Provider gets flights with not so good layovers.

Whereas a member of the tour who chooses to get their own air has no trouble getting Non-stop flights between the same 2 cities?

How does Clark feel about getting your own Air as opposed to letting the tour do it? There seems to be little difference in price.