Would have to know the rates they are getting for the loads and compare to the rate on a per mile basis they are paying. Also have to factor in that on a per mile basis, carriers also pay for the deadhead. On a percentage basis, they usually do not. So you need to look at your cost per mile to operate and figure which way will give you the best revenue per mile and go with it. Ask that reefer outfit to see typical rates they are getting for the loads. If they will not show you, then say adios.
Assume they are the same. The ability to choose is for driver retention. More choices = less turnover. My suggestion is to try percentage and watch carefully. If it doesn't equal per-mile hopefully you can change.