So, I assume you would say that "Your name is Jack", and "She said she would marry me" are indirect questions, because they contain various "realizations" of "Is your name Jack" and "Will you marry me?"
No, I wouldn't. When an indirect question is built into a reported speech sentence, it is introduced by either a conjunction ('if, whether' for general and alternative questions) or a conjunctive pronoun (who, which, what, etc)/adverb (where, when, etc for special questions).
So, your example "She said she would marry me" doesn't meet this requirement.
I assume that you don't see that the first two of your sentences above refer to a question in the person's mind, and the third is an assertion that someone told him the answer.
Again, you refer to the whole sentence as an indirect question, and in my opinion the indirect question is only a fragment of the sentence.
So "He told me what the matter was" has an indirect question as its reported clause.
A phrase is not a single semantic structure if it plays a different semantic role - one in a question and the other in a statement, otherwise any sentence which could be translated into a question would be a question while, by an intelligent definition, it is not.
"Your name is Clark". I know this. It is not a question, indirect or otherwise.
"Your name is Clark?" is a question.
The "semantic structure argument" is either meaningless, or you have not presented it faithfully.
I'll leave this piece of philosophy without any comment as I think I clarified my position above.
Could you give me an authoritative reference that states that simple indicative statements like "He told me where the keys were" is a question?
I don't think referring to authorities can serve as an argument in a scientific discussion.
Your proposition that such a direct statement is an indirect question is outside my field of experience, and I find it pointless to argue that black isn't white unless you give me some good and well-argued reason to believe that it just might be.
Life is too various to be looked at as a black and white dichotomy. 