Bind and fly aircraft with SAFE are built the way the company wants them to be built. That doesn't mean they have to be built that way. But any time a transmitter channel is used a receiver channel is also used except is special mixing situations on specific transmitters. But that's another story. Just remember, if you are going to use a transmitter channel then use the receiver channel assigned to it as well.
Regarding SAFE, it has a mode input that an be set for permanently on or off, either of which, contrary to Prof100, is in my opinion dumb. It can be connected to ANY UNUSED transmitter/receiver channel. So let's say you went out and bought a P51 with flaps and retracts and a Spectrum 6 channel radio. You made a mistake. You need 7 channels or play some games. One solution is to leave the flaps disconnected and use that switch for SAFE Or leave the gear disconnected and use that switch. Either gear or flaps are more advanced options anyway so leaving one or the other disconnected until you get used to flying without SAFE mode is not such a big deal. The last option is to connect SAFE and gear (or flaps) together with a y-harness such that when gear is down SAFE is on and when it is up SAFE is off.

As an afterthought, if SAFE uses 3 modes then flaps also typically use three modes and you could y-harness those. Then set your flaps linkage so you get the least movement until you get used to flying the different modes.