If you keep in gps you won't notice a difference. , different light sequence.
Home lock is nice if you get disoriented. I wouldnt enable manual , just think you would get in trouble with it.
I put mine into Naza before my 1st flight. As long as the S switches are in the upper positions it flys the same. The warnings are to keep less experienced people from accidentally having the switch in the wrong position and crashing. Home Lock is a great tool and Atti can save you from a fly away in some cases. No reason at all not to enable it right away as long as you pay attention to switch positions. The bottom position for S1 is programmable via the assistant and can be set to failsafe or manual. I currently have mine set to failsafe.