Since only (like even, too, and also) is a word with a focussed constituent elsewhere in the sentence, its placement has to coordinate with that focus. The rule for only is that it has to go
- immediately before the focussed constituent
- immediately before any constituent that contains the focussed constituent
- at the end of the focussed constituent (especially if that's the end of the sentence, too).
In this case, the verb phrase have 2 choices is a constituent that may be focussed, and so is the noun phrase 2 choices, and so is the numeral 2. There is no particular difference in focussing on any of them in particular, but if the speaker wanted to distinguish (say) 2, they could contrastively stress it. But this one provides for all senses, and -- because the structure is transparent -- also indicates that which sense one chooses doesn't matter.
And sentence (1) places the only before the verb phrase, thus making all interpretations available. Similarly, (2) focusses on either the 2 or 2 choices, which is again not really a difference unless stressed, and (3) follows the final part of the rule; a comma is common but not required in this case.