Yeah, unfortunately cross-site tools are really lacking; moderators fill out surveys periodically regarding possible tool additions and cross-site compatibility has been my request every time since I became moderator.
For now, I only really see 3 options which are viable:
Post a similar answer to that which is on SO, with reference (like you did), and edit to improve the question so that it is a good fit for the site.
Migration: a moderator can try to migrate it, but if it gets closed on SO then the migration is automatically rejected, and you come full circle to the original situation. Theoretically I suppose an IoT mod could ask a SO mod to migrate the good question over to IoT, but then SO would have to make a policy that IoT questions are off-topic; otherwise they are going to have the same problem that we're having right now (they can't mark new questions as duplicates of our question).
[site-scope] I suppose the other option would be to make a [site-scope] discussion where we could make community policy that questions which have better counterparts on SO are off-topic. The trouble is that it gets pretty subjective (what counts as better?), and they don't become true duplicates, since if their score is too low they'll get deleted by Community. Not saying it would be unworkable, but it would require a lot of discussion (for instance, does the question on SO have to be answered? What if the question is 2 days old? etc.)