Hmmm....now that I re-read it again I see that it's wrongly stated. I meant to say that it would cancel out the weather-sealing benefit of the 70-300 which you stated as one of the 2 benefits of the 70-300L. In other words, with an extender the 70-200 is still weather-sealed and the only remaining difference is the smaller size of the 70-300. (but then the 70-200 would be an f4 lens, so that's a major benefit as well)
In conclusion, buying the 70-300L next to your 100-400 and 70-200 f2.8L IS would be only logical for the size-reasoning in my opinion.
I hope my idea is a little more clearly right now? [A]