It seems like both versions of 龹 exist in different fonts, but considering it basically never appears alone, except in discussions of kanji components, I doubt most people are aware that there’s any variation.
Small variations in fonts are common (see this other discussion from earlier today). But also keep in mind that WaniKani plays fast and loose with components, favoring mnemonic creation over historically accurate kanji component breakdowns. So in other cases, differences might be chalked up to WK just choosing something that looks close enough.