For unknown, svn, reasons extension hooks are not loaded during upgrade
(this doesn't apply to drupal modules) - this causes some fairly serious problems
1) settings are re-loaded & cached with settings from extensions being lost
2) trigger alter hooks are lost this means
 - the summary fields triggers are frequently lost on upgrade
 - hooks that unset various tables to prevent them from being logged can fail, resulting in those log tables being created
 - hooks that specify the table should be innodb can fail to run, resulting in archive format.

I can't think WHY we do this? Presumably there was some problem that would have been better solved another
way but which was solved this way?

Fix "Load hooks during upgrade mode" (45312e1e64dd6af0281fe5fb7f96dbd8be39e524)

In my testing, the commit doesn't do what it says because the symbols are wrong.