There's only one thing to be gained by programming all of the frequencies associated with a site (or sites in a simulcast system). That being if there's a change to the system and a voice channel is becomes a control channel, you'd still be able to receive the system. The odds of this happening are exceedingly remote.
Having said that, there is another condition and the odds of this happening are even more remote. There could be a trunking system controller failure. If that happens the trunking system goes into a "Failsoft" configuration. See: Failsoft - The RadioReference Wiki
If a person wanted to, they could program their favorite system as a conventional system just in case (locking it out until that July snow happens). All of the frequencies would need to be programmed because they are subject to being used in the Failsoft configuration. Unfortunately, programming a scanner for doing this isn't something that can be done through a data import.
(There's a side benefit of this too. If someone is having trouble receiving a trunked system, turning on the conventional/failsoft programming is a good diagnostic tool. If you can hear it as a conventional system you know the system is "on the air" and it is received.)