Unless he's outright lying, this line really makes it sound like they have no plan to merge the two:
For now, but who knows about the future. Also, it could be done a little at a time. Look at the changes over the years to the Mac OS, there has been subtle and not so subtle changes to make it a little more like the iOS. iTunes, Airport, and Disk utility to name a few.
Cook just gave the clearest, most coherent statement that iOS and Macs will never merge, but it will fall on deaf ears here.
I get what you are saying, but the your statement is a little silly if you think about many other things people at Apple have said. Also, thinking that Apple leadership has that decision set in stone is a little naive.
Lets look at some other things Apple's leadership have said in the past few years...
No one would buy a phone larger than 4"
Products in the pipeline. (many times)
The last Mac Mini update (downgrade)
ATV4 will revolutionize how people watch TV.
iPad Pro -“I think if you’re looking at a PC, why would you buy a PC anymore? No really, why would you buy one?”
The iPad doesn't get PC viruses.
Courage to remove the audio jack on the iPhone 7, while lacking courage for keeping on everything else.
Anyways, I hope you are right, and Cook keeps them separate. But, I wouldn't be surprised if it happens anyway.