If Canon was smart, they would have built the lens modular and have an optional version with a flip-in 1.4x like the 200-400.
It will be difficult to use the same lens system in a "modular system" as in the stand-alone 100-400 since the 100-400mm glass will be further away from the sensor when the empty flip out housing is between it and the camera. A flip in housing will be bigger and heavier than having a separate external TC.
So, perhaps Canon has been smart after all and have realised the technical problems and also know that a flip in 1.4xTC will significantly increase the length and weight of the 100-400 so that it will lose its portability advantage, and such a version will appeal only to a few.
Canon 100-400 II
Canon 100-400 II + 1.4xTC
Canon 100-400 II + flip in 1.4xTC
94x >220 mm
> 1795 g
105.6 x 257.8 mm