This is why:
https://m.youtube.com/watch?v=PZryE2bqwdk
Kids internalize that shit and then it stays with them as adults (as the Twitter video in the OP talks about). It's completely unnecessary (as you yourself admit to and illustrate by pointing out how many other changes they make anyway, rendering this specific change all the more unnecessary, reckless, and harmful) and thus should be done away with, as this is the type of shit that subconsciously reinforces racial biases from a young age.
And if you don't like that, there are any number of studies that show the same thing. Just bringing one up from a recent university class I took:
http://escholarship.org/uc/item/5mm8q8f7#page-1
All that, just from a brief exposure from an African-American individual as a criminal (click the link if you want more info about how it was set up or whatever).
Here's another, conveying the same thing (unlike the former, this one's behind a paywall if you don't have university/library access to the journal but I've quoted the relevant bits to this discussion):
http://journals.sagepub.com/doi/abs/10.1177/0093650215579223
And there's much more where that came from. All of them showing that while individual incidents might seem harmless and like they might not have an effect at all, this isn't the case at all, and especially cumulatively, the effects the media we consume has on the ways we perceive one another can be quite profound.
The point being of course, this type of thing can very easily be avoided, and not doing so leads to harmful effects, so that's more than enough reason to ditch the trope to me, at least it should be. No harm is done by ditching it (since there are so many other options that convey the same exact meaning regardless) and there's one less thing to reinforce racial biases (of course, before you try nailing me on this, of course doing this won't solve racism or anything, but it doesn't need to. Anything that helps, no matter how minor, is only a good thing, especially when nothing is lost in the process), so that seems to leave little reason to keep it around.
There's simply no reason to continue a trope of a character turning evil magically altering their skin tone in addition to their clothing and aura or whatever, knowing the harmful effects that shit has. None.