1) I don't think that you have missed anything or that you should really be concerned about it too much. Even without exhaustive research, people who know a lot about kanji know that these readings stand out as being special. Perhaps one of the readings is used in two, rather than just one word, but the sound would still seem unique in comparison to the variety of words used with the other readings. So, I hope my 90%-sure "yes" can set your mind at ease?
2) This link goes directly to a page with a list of kanji with readings that appear exclusively in one word.
3) Are words like this still being created? Yes. To what extent? That's a more difficult question. People are still doing it quite often for names, and I imagine it happens with some frequency as new words are created to describe things (e.g., in science). It's hard to quantify, especially because I wasn't able to uncover a list of 'new words' in Japanese. 日本語の新しい言葉/日本語のつぐに作った言葉とか.... These google keywords don't turn much up, but I'll try to be more creative for your cause and do a little more searching.... Anyway, I hope it's sufficient to say 'it's not a dead practice'.
It seems to me, the reason people use these "distinct" readings is because they're easier to say. I think some strange English sentences are thought of in the same way. You can tell by saying tongue twisters. They force your cheeks to go in-and-out, or your tongue to thrash to-and-fro in such a meticulous manner. For strange English sentences, saying them normally has the same effect. In Japanese, try saying "MOkuNOha", then "KInoHA", and then try saying "konoHA". The upper-case indicate open cheeks, and the lower-case indicate closed cheeks. It's easier to move your cheeks from in to out, rather than out, to in, to out, to in, so I think we just elect this simple variation.
