I think what people mean by "flat modifier" is "a buff to all your damaging abilities" with the opposite being a Mastery that only benefits certain spells. Now, the new Destro Mastery isn't exactly that. It doesn't benefit pet damage or damaging trinket procs. But it's close enough that I can see why they'd use the term.
What I can't see is why they're opposed to it. A Mastery that only benefits certain buttons encourages all or nothing builds; either you stack Mastery to the ceiling and make your entire rotation about pushing those buttons as much as possible, or you ignore those buttons as much as possible and the value of Mastery drops to less than Vers. Neither dynamic is one I'm particularly fond of, because they both make some of your buttons feel weak to push and they both heavily devalue a lot of otherwise interesting talent choices.
I've got enough alts that I'm rather sick of both those extremes. A Mastery that's a more universal "flat" boost to performance, just like all the other secondary stats? Fine by me! Maybe that means I can stack something besides Mastery for once. Or heck, maybe I won't want a single stat at the expense of everything else. That'd be great.