You could say the same thing about switching Jay Garricks.
No, you couldn't, because that's something they spent a good deal of time setting up, so it fits organically into the version of the narrative they were telling. If you'd never read a comic book or seen a DC cartoon in your life, you could've followed the progression of the story and it would've worked as a payoff for what had come before. The storyline of the season was designed to build to that outcome. Changing a "2" to a "3" and a "3" to something else would just be a random and gratuitous change.
But it's turned out to have more in common with comics Earth-3 than with comics Earth-2.
That. Doesn't. Matter. An adaptation is not the original. "Adapt" means "change." An adaptation's responsibility is to serve its own internal story logic and integrity. If it uses ideas from the source, it adapts them to fit the needs of the new story it's telling.
Again: Maybe a half a percent of these shows' viewers, at most, actually read comic books. Probably only a certain percentage of that half-percent would be familiar with Earth-3 in the comics. So it doesn't matter what the comics did. That's not the overriding priority for the show.
Lots of ideas in comics adaptations are amalgams of elements from various different things, rather than exact copies of a single thing. For instance, Batman: The Animated Series's Dick Grayson was a blend of Dick and Tim Drake, and The New Batman Adventures's Tim Drake was pretty much Jason Todd in all but name. In this case, what the television series needed was an alternate timeline that could fill whatever alternate-timeline tropes they needed it to fill. So it had evil doppelgangers of heroes, it had comedy doppelgangers of various people in incongruous roles, it had retro-future tech, it had blimps (alternate universes always need blimps), it was whatever it needed to be. It wasn't about slavishly copying any single thing from the comics, it was about taking whatever they needed from any and every alternate-timeline story in the comics and putting it together into their own thing. The comics aren't holy writ, they're just the raw material.