An effect of a spell, say the STR penalty from RoE, is the total numerical value that is to be applied as a penalty.
It is not two separate effects, one from a random random variable (die roll) and one from the linear level dependent addition, but one penalty to STR (That happens to be a function of a fixed part and a variable part).
The magic missile example just stress that this is the correct interpretation and is hopefully why it was chosen.
Claiming otherwise is rather silly and the aberration on the Simple Q&A thread that did does not deserve any popcorn. (The arrogant fool probably did not even bother to check the PHB.)