Calculation for "Node burn time" field from Maneuver Node Info window based on constant TWR in time of burning. But in reality TWR is increasing constantly when engine is on. Exact formula for node burn time should be next: Tburning = Isp*(1 - EXP(-dV/Isp/g))/TWR.

You might even take into account that the current stage won't be able to perform the entire node and also take into account the situation of the next stage (and may be even give an error if you do not have enough delta-v all together).
By the way I did the calculation myself, and the formula is correct. However it might be good to note that the value for TWR is equal to the initial value, since it isn't constant.

Of course, TWR in formula is initial value of TWR. I special did not highlight more complex situation as you described. RemoteTech flight computer does not work with so complex action, only start engine for desired time.

I would aspect that it could be done, since I know Kerbal Engineer Redux is able to calculate the delta-v of each stage (also the remaining delta-v of the current stage inflight). The only other thing you would need to know is the thrust and Isp of each stage, but should not be that hard.