It's true that for users with less than 3000 rep (or 500 on beta sites), "Other" is not available as an option for a flag, whereas it is a close-vote option above the rep threshold. The only people who can deal with "other" flags are moderators, so you need to use the "moderator attention" reason. There aren't usually two routes provided to a particular action. Flags are dealt with by moderators (on the whole), so since you can't vote to migrate you can only ask moderators to have a look at the question.
However, once you gain the reputation to vote to close questions (rather than merely flag), you do get the "Other" option and can write in a reason.
Questions should be closed by casting close votes if:
- they are sufficiently similar to existing questions and would be answered identically to them.
- they are unclear, too broad, or otherwise problematic to identifying the problem in a way that can be properly addressed by answerers
- they are sufficiently off-topic, as outlined in the help center.
Note that once you gain the reputation to vote to close, you should no longer flag for moderator attention to have questions closed or migrated. It is your responsibility to vote now. See also: How should my flagging change when I gain the ability to vote to close?
That implies that if you cannot vote to close, you should flag for moderator attention instead. That should offer you a write-in box for your reason for flagging: please be as specific as possible. Note that even the full vote-to-close options do not include any other sites except ELL and Meta.ELU, so if you believe a question should go to a different site you will still need to raise a flag.