This is true for any OS (with the possible exception of OSX, which I don't use, so I'm not going to make a blanket-statement about that). Use Windows and consider how consistent apps look there. Hint: They don't.
Look at Android and see how consistent things are there. Again: They aren't. Same with iOS.
No widely developed-for OS on the planet has a 100% consistency rates with conformance to HIGs (nor near 100% for that matter).
Why on earth do Linux DE-developers, the most fragmented of them all, on the most fragmented of all platforms, think they have a realistic chance of getting consistency nailed?
Why are they wasting time, theirs and other's, on this widely unrealistic and meaningless goal? Theirs, I could be willing to accept. Other's shows a lack of respect and understanding.
And what fuels this lack of respect? The importance of "the brand". To be honest, every time I read "brand" elevated to something ulterior in that article it made me cringe. Has marketing departments taken over FOSS? Doesn't the developers see the destructive force they are unleashing on the community?
Seeing all this wasted effort, bridges getting burnt, etc. It's just such a shame.