You’re right, I encountered “fungus” a while ago with an AgfaChrome stock. And indeed, it looks very different, more organic, than the cracks you are noticing. Presumably it was caused by covering the Agfa stock with bee wax or something similar to let it run more smoothly through the projector. It also has the property to grow over time.
These cracks you are describing I have never seen in film stock so far. If they are indeed cracks, your best bet will be to use a proper integrating sphere. Not everything which sails under this name is actually acting as an integrating sphere - this requires that light is shining through the film from basically all directions possible, covering a complete half sphere. Also, the distance between sphere opening and film should be minimized as much as possible. Otherwise, you will loose the extreme angles coming from the light source.
Even better is to pair this approach with a wet gate. Basically, the cracks in the film are filled with fluid having the same or a very similiar index of refraction as the film stock. If that is the case, the wet film looks to your camera like a film without any cracks or scratches - if the cracks/scratches have not disturbed the original film layers.
Your cracks shift position from frame to frame - therefore, any temporal cleaner should be able to handle this. As your NEAT example shows, the cracks are gone after processing. Here’s an example using the “Automatic Dirt Removal”-tool from daVinci (frame 91)
I had to reduce the “Dirt Size Thr.” down to 0.01, from the default of 0.1, in order to obtain this result. Temporal radius was two frames, motion estimation type “Better”, the remaining parameters were at their default settings.