Her Majesty The Queen

"Her Majesty The Queen" appears to be a confusion of meanings, majesty being a thing and queen a person. What enlightening did I miss ?

Not at all. Although majesty can be used as a noun, in this case you're looking at established historical usage. As with H.M.S. (Her Majesty's Ship) Pinafore, this is an honorific label steeped in the tradition of monarchies. And England isn't the only monarchy that does this.

I've always had a notion that referring to a person by a title such as "your majesty", "your highness", "your Worship", "your Honor" and so on had its roots in the sense that it may be impolite to say just "you". So one refers to his Eminence in the third person, you see, and it became a tradition, at least for some titles. It's just a notion, though.

Yes, tradition and customs always rule, and just as well. Only a part of my brain that stays like a child sees a situation in which the Queen commits a crime and says “Oh it's not me, it's only my Majesty that did it!â€
I'm surprised that this is thought exceptional, as it isn't just a facet of monarchy but honorifics in general, and especially as the U.S. retains titles like “His Hono(u)r, the Judge†- indeed, I read on Wikipedia that: ‘the Superior Court of Los Angeles County, the largest unified trial court in the United States, has a rule that the judge shall be addressed only as "Your Honor", and never as "Judge", "Judge (name)", "ma'am", or "sir".'