Advantages? Easier & quicker, less memory used in your scanner. Disadvantages? Not much, really. Fleetnet is a mature system and it's pretty well known what the alternate channels are... so it's unlikely that you will get hung out to dry by them switching to something that you don't have programmed in.
Some P25 systems (especially Harris systems) can use any channel for a control channel, but this doesn't apply to Fleetnet.
The one advantage of programming all the voice channels and NOT using control channel only...if you are using CC only mode, the radio will automatically calculate the frequency to tune to for any voice comms. This is fine, except that scanners are notorious for false decodes - often your radio will get told to go to a voice frequency that is incorrect, resulting in garbage on the speaker.
By programming all the frequencies and not using CC only mode, you significantly reduce the possibility of that happening. The downside of course is that if they ever add a voice channel, you're SOL.