I would be interested in the ability as well, at least in the areas where it doesn't apply to my media. Possibly have a switch in the conf that can bee added to folder paths as an opt out option.
I have my media sorted into SD and HD locations. Transcoding options in folders that don't require any transcoding just confuses the situation. While ExSport may have a point in that you can just ignore it, I would like to see the option exist as not to confuse my end users. Not all users of the end result are going to be tech savvy, and simple and slick is the best offering for the average user.
Often, if you are like me, you have already done a lot of post work on your media to ensure a lot of configuration isn't needed. I have over 600 items in my SD media area, every one encoded with the same codec, which required a single transcode with some software and never needs to be done again. Sometimes I also pass HD content through similar methods so that a simple click and go is all that is needed, and turning on options is the exception.
A lot of waffle there really, but basically I'd agree to an option to have it apply only to folders you wish it to be in. Not sure how you would achive this if you were running the media library option, but I'm sure there is a clever solution somewhere.