If the provided application-id is not valid then it will not be set. I'm not familiar with the glibmm bits, but if you don't provide an ID to g_application_new then, according to the documentation, "...some features of GApplication (most notably application uniqueness) will be disabled."
"Suppressing" it is easy--just fix it. Provide a valid application ID or don't provide one at all (pass NULL instead of a string). In your example, getting rid of the extra dot ("org.gtkmm.examples.base" instead of "org.gtkmm..examples.base") should do the trick. The g_application_id_is_valid documentation explains what constitutes a valid ID, including that "Application identifiers must not contain consecutive '.' (period) characters."