If these two methods were implemented with more fidelity to the interface they belong to, I think Composer Button Bonanza would pretty much “just work” in the new RTE (at least as well as it does in Markdown mode). I’m surprised that no other theme component or plugin authors have raised any related issues yet. (Though, maybe they have; I have not tried searching for similar complaints.)
I don’t know what “all the power of ProseMirror” entails, but I doubt that is necessary. The applyList() and applySurround() interfaces are not that complicated — though there is more to them than what has been implemented so far.
(What has been implemented so far appears to be not so much a principled “apply list markup to the selection” or “apply text markup surrounding the selection”, but more “just dispatch the calls from the known, built-in toolbar buttons to specific prosemirror functions”.)