Yeah but all the elemental matter in the universe is like three dust specks floating in a lecture hall. You can ask about the dust specks or the lecture hall interchangeably.

This is a common misconception. Intergalactic space is filled with about half of the matter in the universe. See: https://en.m.wikipedia.org/wiki/Warm–hot_intergalactic_mediu...

As to your original point though, there doesn’t appear to be too many elements here apart from ionized hydrogen and hydrogen.

Great point. I almost missed this. It really seems like there should be another separation in the article I linked, between "Universe" and "Milky Way."