I've never received points in any program when my company direct bills my stays (usually about 3-4 times a year when we have congregate staff training or meetings.) Usually the hotel and company, at least in my case, have negotiated rates, ameneties like free or reduced meeting rooms, and contracts which cause the rate to fall out of the terms of what the program covers.

I remember in the early years of programs in general, a couple of chains tried to eliminate giving points on government rates. It didn't last long.

The other issue I suspect happens with direct bills and loyalty programs is the issue of the purpose of the program. Direct bills already serve the purpose of creating business because in most cases the loyalty is already created/mandated by the company. The loyalty program exists to attract and maintain those guests who have a choice of where to stay.