So what I'm guessing has happend is that these were busted symlinks from
sometime ago. And since the links point outside the currently supported
inidir (which is /etc/php/7.0/mods-available as you noted), the
purge/remove scripts are refusing to delete them. The packaging is
basically treating those links like user-local customization, correctly.

I am  unable to reproduce the issue with 16.04 release, can you confirm
that? On purge, I do get a warning:

dpkg: warning: while removing libapache2-mod-php7.0, directory
'/etc/php/7.0/apache2/conf.d' not empty so not removed

which might be the problem you are seeing too (and dpkg is doing its
best to tell you manual intervention is necessary).

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https://bugs.launchpad.net/bugs/1578225

Title:
  apache2 php7.0 conf.d links

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