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Databases are not the issue but that the updater doesn't handle it... My personal instance and our work instance never take long (a few seconds) to fix the database. I mean the instance is already in maintenance mode and adding a checkbox to do it or not to do it, should be simple. I don't know if there are instances where it takes long and its better to do it during the night.
I've made an update script that tries to run the migrations and index updates in one go.
The updater itself is by far the slowest of the three commands. I think downloading the new version into a different folder and just moving apps and files over would be much quicker. But I haven't had the time to look at potential errors with that method.