I would rather have my ability to select a car from Emerald Exec Selection and get rental credits over being assigned a car and getting FF miles with another agency. Lots of companies have multiple rental car carriers; I have yet to be stuck only with one.

You were expecting somebody here to have magic that will stick your firm with the cost of paying U.S. Federal excise taxes on miles & promo miles? That's why firms negotiate ineligibility for miles with National. Corporate travel staff may care about price and service reliability but they're not likely worried about helping you accumulate FF miles.