It seems Kindle Comic Creator creates dual-MOBIs -- these are .mobi files which contain both MOBI and AZW3 sections, in order to work well on new devices and also fallback on old devices which don't support AZW3.
Unfortunately, manipulating the metadata in one appears to be a PITA.
KindleUnpack can split these apart, which will also save wasted space on devices which support AZW3.

You can also try
mobiperl, which contains the core manipulation tools including mobi2mobi. What you are thinking of as mobi2mobi is actually
a GUI frontend. But I have a feeling it will do no better than calibre at manipulating the EXTH fields in both sections (i.e. the AZW3 section as well).