I strongly recommend you go over to
https://www.gemologyonline.com/Forum/phpBB2/index.php
I'm going to post a link here over there and see what happens.(also, they have a sub-forum specifically for gemological photos of gem inclusions, i.e., any imperfections inside a gem one can see)
There are best-in-class gemologists there, including some with heavy interest in physical chemistry, geochemistry, optics, and instrumentation. I think they would be able to actually answer some of your questions. Or tell you "it is unknown"... with some degree of authority and certainty.
I mean... they LIKE real scientific publications and some are real (professional) scientists that do gems for fun or a living. (disclaimer- I was active there 5+ years back, the "good" folks may not be around anymore)
From the little I know about this stuff, I'll note that natural gems are formed under non-ideal conditions. Crystal strain, partial fractures, partial healing of fractures (by partial melting), crystallographic dislocations, and many more are all well-known to sceince-oriented gemologists. Then, there are human- caused issues like subsurface strain caused by plastic deformation during polishing... fracture-filling... very high temp treatments in varying redox conditions and so on.
The bottom image looks kinda like partially healed fractures ("fingerprint" inclusions); the top... dunno.
I have seen other SEM images of polished stones, but none looked anything like these. It is possible even that the images are in essence artifacts of the technique, making interpretation of the data ... problematic.