Warning: this question relies on anecdotal evidence.
I have noticed that often Chareidi and heterodox Jews will wear much larger kippot than Modern Orthodox and Dati-Leumi (and heterodox rabbanim). Is there any rationale for this?
It's not clear which practice you are looking to find the rational for, the larger or the smaller, but see the first tshuva in the Igros Moshe where he discusses Reb Shlomo Kluger's ruling to cover the majority of one's head. Reb Moshe says that it is a nice stringency to keep, but one is not obligated to be stringent, especially since most people are not stringent. As opposed to the need to wear a head covering while sitting around which is also a stringency according to the shulchan aruch, that is a stringency one must keep being that everyone does it. And especially in light of the ruling of the Taz who says starting from his times being bareheaded falls under the prohibition of walking in the paths of the nonjews. And of course wearing a head covering while walking 4 amos or saying Hashem's name or walking into a beis harnesses which requires a headcovering by law.
But the point I'm tying to bring out is covering a majority of one's head is a nice stringency but not binding, hence the various types of kipot and yarmulkas.