I'm not entirely sure what you mean with a neutral position causing ambiguity. Even the two "neutral" examples you posted (aliens & explaining downvotes) would seem to be clear cases where votes can be used to express agreement or disagreement:
Should aliens be allowed to answer questions?
- Upvote = For - Yes aliens should be able to answer questions
- Downvote = Against - No it's a ridiculous idea
Should we explain downvotes?
- Upvote = For - Yes, it's a good system and should be implemented
- Downvote = Against - No, let's not do that
I just don't see where the confusion comes in.
You're quite correct that those two questions don't in themselves lean to either side, however votes can just as easily and straightforwardly be used to express an opinion on the issue as if they were phrased "We should prohibit aliens from answering questions" or "People should be forced to explain downvotes". The outcome is the same.
Finally, to address your reversal concern:
Here is another reason why this can lead to confusion, the user could modify the question to "Should we not explain downvotes?". Which will swap negative/positive score if we voted based on dis/agreement.
You're right that this could possibly swap the tallies, however I would anticipate that such an edit would be spotted fairly quickly, deemed malicious (or at least not in the democratic spirit!) and rolled back without further incident.