It has never been standardized, because we have never successfully defined what does "exceptional" mean. In your case, you're speaking about stops which are "rarely served" (but they may be served multiple times a day), is it exceptional? Is "exceptional" a station closed for 10 years? 5 years? 2 years?
My 2¢ for your issue is that you should rely on data consumers to have a great UI handling this use case, and I do not see an easy way to extend GTFS to handle your use case. I am personally always strongly pushing against notes fields, because many things can be added in notes, and nothing is harder for data consumers than to decide where and when to display a "note" field.
— Leo Frachet | fr, en, de | Executive Director of MobilityData IO | mobilitydata.org