Qavion
A couple of points re' the 744 throttles.
1. They are ALL driven by a SINGLE servo motor so if they are physically staggered they will remain so unless they are signalled to fully closed - they would then pick up equal positions again.
2. The throttle trim works to trim EPRs or N1s against the value set on the second highest engine. It is effective for a specific engine ONLY if its throttle knob is within half a knob's diameter of the remainder. For your hypothetical situation, the backed off engine would not trim.
As far as the potential overboost is concerned, there should be no problem if the EECs are in NORM as they will automatically prevent overboost and spool speed exceedance - throttle physical position doesn't come into it. The power set for GA will be whatever shows on the Primary EICAS as the GA reference thrust.