Dvorak keyboard's fatal flaw is when you have to type on someone else's keyboard. Standardization has its benefits, even if less than ideal. Trackballs have a similar issue.

I've exclusively used Kensington trackballs at home and work (along with trackpads on laptops I guess) since I was around seven years old, Dvorak since I was around fourteen.

I really don't use other people's computers that often, but mice aren't that hard to use (just uncomfortable) and I can still type in QWERTY at about 25WPM but I'd have to look at the keyboard a bit.

Trackballs and Dvorak are both more comfortable than their alternatives, but the real benefit is the reactions I get when other people try to use MY devices when they're not prepared lol

To an extent, Vim and Emacs have a similar issue, especially if you spend time customising these.

Often, the benefits from using an improved tool outweigh the costs of it being non-standard.