Yes, this bug has not been fixed yet. The biggest issue I can see still comes back to - what to do to fix this, without breaking existing levels?
One possibility is to make the editor automatically adjust the spawn order to account for is. However, this doesn't really fix anything, it just works around it in terms of what data it saves.
The other possibility is to put some kind of flag in level files to identify them as ones created after this bug was fixed; and only apply the bug fix to these. This would still potentially create problems if using an older editor version - and still require an editor update.
Another possibility is to simply fix it, and leave it up to level designers to account for it. This seems inconsistent with the goal of ensuring portability between versions as far as possible, especially for content made prior to the fix.
The last possibility is to simply leave things as is (at least until the level format is replaced - I still plan to move to a text-based format eventually), and make sure it's a well-documented behaviour. This would have no impact on compatibility, but may be slightly counter-intuitive for those who are not familiar with the behaviour.