I think you may have taken what I said above out of context there. What I was saying is if that is the way you are performing your upgrades every time, it is not the correct manner in which to upgrade. If there is a reason you are doing that, then this is really what needs to be addressed. Whats happening at present is it seems you are upgrading in a different manner to try and work around an issue, and in turn causing other issues (in this case multiple sets of tables). When really, you need to get the original issue resolved.
Upgrades should really be painless to do. Of course, as mentioned above, we cant account for every scenario. There will be instances where 3rd party items cause an issue, where hosting doesn't fit with the latest release, or indeed there is a scenario specific to yourself that is a bug we need to resolve. But in any of those scenarios, it should only be painful the once.
My advice at present would be if you have an issue with the automatic upgrade process, once you hit that issue, call out. Don't try to work around the issue. Also, do yourself a copy of your site using your test key. This way, if you are having issues, you can do a test upgrade on your test site, before upgrading your live site.
We are here to help you at the end of the day, and if we arent aware every time, the issues will continue to occur.