SAME. HEIGHT.
You forget that in the soul room Yami is taller than Yuugi. What about the episodes that show them there? Yami’s always taller. Also, in his own form hes nearly as tall as Joey and Tristan.
Not in the manga. Yami (and Atem) is always the same height as Yugi. Whether it’s as above (one in body, one spirit), in the soul room or in Millenium World. Literally every panel they’re next to each other they’ll be the same height.
The original idea was that Yami gives off the illusion he’s taller because he stands straighter. He’s confident, so he stands shoulders back, back straight. Whereas Yugi is shy, so he tends to hunch. But if you put them side-by-side, they’re the same height.
The anime took the ‘Yami standing straighter, looks taller’ a little too far by making Yami’s height… entirely different depending on the episode. Sometimes they’re the same, sometimes the difference is minimal, other times Yugi comes up to his naval for some reason. But in the Memory Arc and the final duel, when they’re mostly separate, they’re usually the same height.
TL;DR, Yami’s a short mofo too, the anime just mucks this up a lot.