The autolinker avoids certain extreme edge cases by design, last time I mentioned this to @Vitaly the general recommendation is to use <.......> here for terrible edge cases which allows you to workaround this. Does not work with one box though.
Since linkify-it uses heuristic, it can never guarantee 100% confidence (even 99.99% != 100%) => it requres some marker (currently <..>) to force link borders.
Your onebox also requires some marker to force on/off.
So: you have two independent processing modes => need 2 independent markers/flags to define.
Currently, you have only single marker for 2 modes. That’s a logical collision. In my project i solved problem this way:
Allowed to apply link convertor to autolinks (<...> - this markup).
Added checkbox to editor options “disable links expand” (for every post)
Not ideal, but ok for me. My be you can invent better way how to add second markup/flag for your case.