Semantics...
How the hell do you fuse 2 eyes together? Show me that. Furthermore, how would, a blind, Madara knowingly 'fuse' the pair of eyes? Especially if there was no precedent of it happening before him. Just grab his brothers eyes and blindly smash the pair of eyes together in the sockets & hope for the best? Or perhaps he pulled out a scalpel, seperated the corneas & lenses and merged them together that way? Please, it's more logical that he would take his brother's eyes, switch them out in their entirety & connect the tendons & nerves with basic medical ninjutsu.
As for the argument of the EMS having a mixed pattern? Take Itachi's eyes, put them in Sasuke and as his blood, DNA, chakra etc. mix or 'fuse' with Itachi's eyes, they become something unique. A mixture of the two.
Why was Kakashi able to use his eye right away and Sasuke had to wait it out with the bandages on? Well first of all, Kakashi's eye doesn't work all that well now does it? He can't switch it on/off. Sasuke's work a little better, I think you'd all agree. Who really knows though, it's hard to compare the two since Kakashi isn't an Uchiha.
All i'm sayin is show me, show me how they physically fuse two eyes into one and I'll believe it. Otherwise there is room for interpretation. Semantics...