Are there any significant differences between the two of them? If there isn't, should one of the close reasons be removed to make it less confusing?
If enough close voters (or a moderator) picks the option under “migration”, then the thread (the question, its answers, its comments, their votes) is automatically moved to the target site. Use this for questions which you think are perfectly reasonable but off-topic here and on-topic on Super User.
The option that isn't under “migration” just closes the post here. It leaves the advice that the question may be suitable for Super User, but it's up to the asker to decide to repost there or not. Use this for questions which you think are within Super User's purview but are not suitable in their present state. Typically the reason to pick this option would be that the question lacks some important information (OS and version information, precise description of what was tried, clear description of the requirements, …); you should explain this in a comment.
Or, in other words: migration is when you take responsibility for moving the question to the other site. “Can be asked on” is for questions where you wash your hands of the responsibility.
As they come up in different options I don't think they are confusing, in fact having that first option can make it simpler for newer members to understand the common close options.
The migrate section works better for those who know a bit more about the SE network.