I'm not getting this at all. I have frequently stayed at Hiltons and Marriotts where someone else is footing the bill, and have never had an issue with my loyalty program number being entered in the record, with receiving any elite benefits I may be entitled to, and receiving a copy of the folio at the end of the stay for my records, even if the bill is addressed to someone else.
When you say "someone else footing the bill", what exactly do you mean? Direct billing to a central account, or someone else's card being used (maybe with a faxed authorization)? Off of a normal rate or a rate that they negotiated with the property?
It's reasonably common, if buying enough rooms, to be able to negotiate away loyalty benefits in exchange for a lower rate and prohibit the rate from being shown to guests. That's basically what Expedia does.