Yes, I haven't been able to reproduce this without manually changing /etc/mysql.
But it might be worth adding a check on the result of the alternatives-command 
and having it suggest purging and reinstalling mysql-common if there's a 
failure?

** Description changed:

  We get a fair amount of installation failures due to issues with the
  contents of /etc/mysql, such as /etc/mysql/my.cnf.fallback being missing
  when it's set up with alternatives.
  
- It seems this is sometimes caused by incomplete removal/purging of
- previous packages and not just user customizations, so should be
- investigated further.
+ The most common cause seems to be deleting /etc/mysql after removing
+ (not purging) packages, resulting in files not being rewritten there
+ when trying to install.
+ 
+ The workaround is to run apt-get purge mysql-common to clear out the
+ conffiles properly, then reinstall.
  
  Might be related to LP: #1602945

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https://bugs.launchpad.net/bugs/1612569

Title:
  Changes to /etc/mysql cause installation failure

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