As described in T95671, pywikibot.config2 does issue a warning that the types have changed. The reason for the warning of transliteration_target looks straight forward. It is probably manually set in the user-config as a str (aka bytes) while the original value in the config2 module is unicode.
But I'm not sure why the warning of console_encoding appears. It is read from sys.stdout.encoding which is str (even with unicode_literals) which would explain why it was str but if it changed type and the warning appears that would mean @Wesalius has set the encoding using u'…' which seems unlikely.
Now to fix that we could do something similar like int/float handling so that if the type was str or unicode that it also expects the other type.