The priority function operates differently when you are scanning conventional channels vs. trunking systems.
For conventional scanning, such as your railroad freqs, designating a priority channel will make the scanner check a specifically programmed *channel* every two seconds to help ensure you don't miss an important transmission if you are sitting on a busy channel, or are scanning very large amounts of programmed channels.
When trunking, the priority function will check a programmed *talk-group* every two seconds - which may come in handy if you are listening to some other talk-group that has a long-winded transmission. At this point, the talk-groups transcend the importance of specific channels since trunking doesn't designate a specific channel to a user - it usually changes. Much more trunking info in the wikis and messages here on RR!
So no, when trunking, you don't want to program a control-channel as a priority channel - it isn't intended to work that way when in the trunking mode.