No--the airlines are always free to send the bags however they want. The rule is that the passenger can never separate from their bags, not that the bags can't separate from the passenger. If you expect the bags to be on your plane you won't carry a bomb unless it's a suicide mission--and that cuts down the number of people willing to do it and cuts down the skill level of the people trying it.

If the airline happens to separate your bag from you you won't know it.

(Actually, though, it does leave open one scenario. Build a suitcase bomb with a timer, clock and an altimeter. Plot a long stopover where there are earlier flights. When the bomb goes up in the air the timer counts off a bit less than the duration of the flight. Once that time has passed the bomb counts off the first stage. Once it's back on the ground this counts off the second stage and the bomb arms, set to explode at altitude. When the clock reaches a bit before your connecting flight the bomb disarms again. If the bomb remains with you for the whole trip it will not explode but if it gets sent on ahead it will.)