I bought the MDX from a Seattle area dealer, saving a bit of money in the process. While I didn't have a great experience with one of our Portland dealers during negotiations, the other was good and so I decided to have my maintenance during warranty done there and, depending on the experience, in the future. The first, A1, maintenance was a good experience at a premium, but not obscene, price. But this one is over the top. I will probably try the other dealer for the remaining half of the basic warranty period. Once the warranty is out of the picture I will only be going to the dealership for problems that need their skills (i.e. damn few). While I have changed a lot of oil/filters in my life, at this point I generally just go to a quick change place for oil. The need for special oil may require some other approach, such as an independent mechanic. Or maybe I will crawl under the car myself - it is no big deal, and the oil is available at a good price at Costco, a Fram Ultra oil filter would be an improvement, and I already have a supply of sealing rings for the drain plug. It is easy to get quality air filters on the web for $25 for the set, and as you have said it is quite easy to do the replacement myself.
As for the cleaning charge, to clean up after a mouse does require enough access to be able to wipe down the air duct to remove the urine residue, or the smell will persist for a very long time (voice of experience here). And if the mechanic just pulled out the old filter I would expect the droppings would fall down into the blower. So I am guessing that the blower had to be removed as a result, and from there it might be possible to reach up and wipe down the duct. I am guessing that the $140 represents one hour of labor, and it is possible that it took that long. My guess is that the SA made the offhand remark about the cost of cleaning before he knew how much time was needed, then chose to sneak it by me rather than explain that he had to charge for it. So the real problem is the way the SA dealt (or really didn't deal) with an awkward situation; I won't argue about that cost because it is quite plausible and I have no evidence to the contrary.
The higher billing than promised for the B16, the ridiculous charge for the filters, and failure to own up to the higher costs for cleaning (not the costs themselves) are the problems for me. The $500 bill had me pretty p***ed-off as it was a surprise after the fact, and it has been helpful to now go back and reflect on it. Had the SA brought it up at the time I would have noticed the discrepancy in the basic B16 costs and the bill would have been corrected by $59 - the rest I would have chalked up to high dealership prices (and would have done things differently in the future). But sneaking the whole thing past me without a discussion was just cowardly. And, as I have said, it certainly was my mistake not to go over the bill before paying - thinking that I knew what it would be is no excuse.
Live and learn...
Greg