Here's a simple answer -- it depends. If the light's not great a TC is out for me, then I'd prefer to crop on post-processing. If it's a small subject (dragonfly, butterfly, etc.) in good light I usually use a 1.4x TC on my Olympus 100-400mm, if there's time to put it on. Out of desperation I've used the Olympus 100-400mm plus the 1.4x TC and the 2x in-camera TC for a FF equivalent of 2240mm which in really good light and on a sturdy tripod might produce a usable image. The newer Olympus (OMDS) cameras have a really good in-camera TC that I've used with my 75-300mm that does not take a TC and isn't sharp enough to allow for much cropping. Andy Rouse has a video on the in-camera TC --
What about the 100-400 with No TC on the mk 2? for small birds where you can't get close but are not unreasonably far away? Have you tried that?
Tom