This restriction has a few exceptions: it doesn't apply
- on Meta sites
- when both questions are asked by the same user
- for ♦ moderators
Therefore, using a custom moderator flag is a good option. Please specify clearly why you're using a moderator flag instead of a regular vote to close; standard flags are always preferred and you risk getting a declined flag otherwise.
Given the relatively low occurrence of this situation, opening a Meta question (as you did) is also an option. Moderators are always notified when a new Meta question is posted, so we're likely to read it about as fast as a flag.
In some situations, one of the questions contains some information which might be helpful to the author of the other one (e.g. some things they have tried already). In that case, it's nice to leave a comment with a link to the 'better' question.