1. You won't miss anything by having the input locked out. The repeater just listens on that channel, and rebroadcasts on the output frequency at a much higher power. The only reason i even programmed them in, was in case my CloseCall picked up the freq, that way i would already know what it was used for.
2. I am not the expert on APCO-25, just starting out myself. First, APCO-25 is just the name of the new standard that law enforcement radio systems have to meet. It is possible to have non-trunked digital frequencies in this mode. Non-trunked digital freqs do not need a control channel, thus working the same was as conventional freqs, just need a digital capable scanner is all. The channel # shown by them is only for internal use at the PD(ex: switch to channel 3, Bob, there's a hot blonde at Mike's.......) Digital frequencies dont need tones either.
Hope that answers your ?, someone else may post here and correct me if i'm wrong.