Real problems have already popped up years ago:

https://bugs.kde.org/show_bug.cgi?id=226630
https://bugs.kde.org/show_bug.cgi?id=246808

So gpgconf could add, for example, "ignore-invalid-option log-file", to the
configuration file if a log-file option is emitted, and then GnuPG2 would still
honour this option, but GnuPG1 would silently ignore it?

So you are saying, every distribution supporting a co-installation should patch
GPG to fix this?
The user might not even know what gpg is, that several major versions exist, or
which options are available where. He just sees email encryption not working any
longer. In most cases, he won't have decided to install both versions - he just
has software installed which, indirectly, depends on both.

Of course it can be fixed by changing the config files. However, the default
behaviour (if I start gpgconf as a new user) is to use the shared config file
for both versions. As I see it, programs are responsible to set up the
configuration in the user's home directory if they need one - at least, that's
common practice in my experience.
If this is not a bug in GnuPG, then whose installation problem is this?