Bonus Bucks are supposed to be treated like cash (and this is what happens 99% of the time in the U.S., as you say). You should get Marriott Rewards points for the gross amount, before deducting the Bonus Bucks.
When using EEO certificates, I have always gotten the full number of nights credited. I suppose that the free night should not be credited, but Marriott's computers don't seem to be sophisticated enough to recognize use of the certificate and then split the stay into creditable nights and non-creditable nights. It may be too much trouble to bother with.
Bruce