There are some really interesting points here. The first pointed out in the original post is, in this case things can still get fucked up, even if you "did everything right"/took all reasonable precautions. A hotel employee made a clerical error.
Another is
don't lie to your employer. (& if you do make sure it is well thought out and you can play it thru to the end) It can get you fired for cause and that will really cramp your style. There are plenty of reasons why you might want to get a room in your home city. The clerk in the travel department doesn't care. Don't make a bigger deal out of it than need be by creating some elaborate story when simply saying "thanks for the call & letting me know," will suffice. People get themselves into so much unnecessary trouble by offering more information than is required or asked.
Have your affinity program statements sent to your office. If they require a phone number, use your cell. & I hope it goes without saying your old lady shouldn't be reading your emails.
As for expedia/priceline, etc. or even when someone else is paying for the room via some direct bill account kind of thing, I always still present my membership credential when checking in. At a minimum I'll get whatever upgrade my status entitles me to. Sometimes I'll get full points etc. too. At worst I'll get credit for the "stay" & "stay nights" which are usually what are used for getting to the different levels anyway (gold, silver, platinum, etc,). They don't give me the points because the points are based on dollars spent and you are actually spending you money with Priceline, etc. It doesn't cost to ask & even if they give you nothing they know you are a regular guest & all the goodwill that comes with that. They also know that regular guests and "point people" are more likely to fill our satisfaction surveys and the 1st to bitch if something is unsatisfactory
One other word of caution.
No matter what she says or how good you are feeling after she just drained every ounce of semen from your body....if the room is in your name, do not let her keep it for the rest of the day/night. Too much can go wrong & you aren't even there to try to control the situation.