That’s not inconsistent, that’s just reflecting how our writing system works. CSS was designed around the idea that there is a document consisting of text, which implies the X and Y axes work differently – because they work differently for our writing system.
Text goes from left to right, then wraps back around to the left moving vertically down (obviously this is for RTL languages; adjust for different writing systems). So this means that there’s a left and a right edge, which means that centring something horizontally makes sense – the mid-point between those edges is the centre. But it also means that there’s no real bottom imposed upon the text – the text starts at the top and just keeps flowing downward until it runs out. So centring something vertically isn’t the same sort of thing as centring something horizontally.
Or to put it another way, the horizontal edges are imposed by something external to the content (often the viewport), and the bottom vertical edge is defined by the length of the content. The two axes are treated differently by CSS because they are fundamentally different.
If our writing system were turned 90° on its side and we wrote downward until we reached the bottom of the page then moved back to the top and right one line, like some traditional Asian writing systems, our browsers would scroll left and right by default and you would be complaining that `margin auto` expands top/bottom margins but not left/right margins. It’s the writing system that works this way, CSS just does what is sensible for that writing system.
Later on, more layout systems like grid were introduced by CSS that weren’t based upon the flow of text, but things made logical sense before then as well.