Finally, the third form is the one that represents the spoken form most accurately.
I disagree, it's normally clear from spoken English that the second option is also something you are being asked about, which is what a question mark represents.
Further, written and spoken language do not coincide perfectly. There are things we can do with one that we cannot with the other. (We cannot gesture with our hands on the page, we can't change typographic choices in speech, as obvious examples).
Where they do coincide is in their purpose; in this case, to ask a question. Most of the time when we use such a sentence in writing, our task is not to reflect speech, it's to find out whether the red dress or the blue shirt is preferred.
The two times when we do want to reflect speech, is in dialogue and transcriptions. Even then we don't want to reflect it perfectly; most people talk in a poor first-draft at best, not to mention all the ums, ehs, broken sentences and so on (if a journalist wants to portray someone as an idiot, they'll record their speech faithfully).
Here, while the first form hasn't been common in writing for hundreds of years, it might serve in dialogue, to reflect the second option coming after an initial question form:
"Do you prefer the blue dress? or the red shirt?"
Even then, we'd likely break the reported speech at that point, to reduce the strangeness, and further emphasise the second part coming as a later thought:
"Do you prefer the blue dress?" she asked, "Or the red shirt?"
The third form would still not be used, because the second part is still a question. Unless it wasn't, but again we'd probably not want to depend on the quoted dialogue alone:
"Do you prefer the blue dress? or the red shirt." It was clearly not a question, the red shirt was the answer she wanted from me.