I don't think this is a particularly well-founded concern.
Firstly, Mattel cannot control the fact that DC can't just settle the fuck down and pick a batsuit. At some point, Mattel has to make a decision on which design to run with for any given figure and if that costume disappears from the comics, or becomes less important, or whatever, during the course of production - that's kind of too bad for Mattel. They can't just stop production and start over with something else.
More importantly, I'd argue that with characters like Batman and Superman, the foundational elements of their design have become so iconic that it doesn't actually matter if you're getting this particular look or that particular look. I'd go so far as to argue that even trying to get comic-accurate costumes at all is more to try to pull in the occasional adult collector.
If a kid 'likes Batman' then all that really matters is he sees something on the pegs that looks like Batman to him. To TSI's point; the Kenner line had like.. ONE Batman that actually matched the cartoon look of the character and I'd argue most kids didn't even own the goddamn figure because it was not very common.