What kind of troubles there could be doing it this way?

I think, I will sleep better, because now each battery's protection circuit protects what it was design to do, each's own battery.

What I see the problem in the first version, was that if I drop the phone hardly and/or it gets really wet, the shot-cut caused by battery2 or by cables will shot-cut battery1 without any protection circuit in between the battery1 and the short-cut. If this would happen, it could set battery1 to "explode" to a fireball.