9v and Power Functions Hybrid?
I'm not so sure using 9V will be usefull ?

My son has a PF cargo train in his room, when he turns it on, it goes, ok.

but even if my son goes downstair to get a cookie while he still has the PF emitter in his hand, then train still runs !

According to me, PF infrared link is used only when you wish to change speed setting, so if you don't plan to slow down your train in the tunnel, you are ok.