If, by "indirect question" you mean a "rhetorical question", then you have provided your own answer. Rhetorical questions may or may not end with a question mark -- it's entirely personal preference.
Rhetorical questions can be phrased in exactly the same way as a direct question. I'm not sure why you think there is some rule to define the difference. Perhaps this is something you have been incorrectly taught, otherwise, why else would you believe it to be true ./?
Now, my personal preference would be to end that last sentence with a question mark. But there is nothing wrong with instead ending it with a period.
Alternately I could have written it without using "would":
why else do you believe it to be true?
and it would still have been a rhetorical question.
It's a little more complicated when the rhetorical question appears in the middle of the sentence. In general, end with a question mark if you want the entire sentence to be perceived as a question (rhetorical or nor). Otherwise end with a period.
Here's a clumsy pair of examples.
You might ask, why would we end a rhetorical question with a period, when it's not a real inquiry that expects a response?
You might ask, why would we end a rhetorical question with a period, but the answer is simply that it's not a real inquiry that expects a response.
The second sentence is fine as written, but my personal style is to set off the question with quotation marks, and turn it into a direct question.
You might ask, "Why would we end a rhetorical question with a period?" but the answer is simply that it's not a real inquiry that expects a response.