They’re limitations. Some are deliberate, some may be tackled in future.
Obsidian can do many things, but there are many things it cannot and some of those are by design.
.folders have always been hidden in Obsidian - and obviously they were designed to be hidden from most users in the OS, so I’m not sure that’s an unreasonable limitation.
Only md is seen amongst the many markdown extensions.
Originally only pdf and image extensions were also visible, though that has been slightly extended.
The txt to md plugin allows you to see and edit other plaintext extensions, so long as you add them to its code, but there was consistent resistance by the devs to adding more extensions to core ( Handle (edit) other plain text file formats ( rmarkdown, tex, txt, code, etc ) ).
The file explorer seems likely to be improved, but, given the above, I’m not sure it will move in the direction you would like.
I do most of my work with the files in Obsidian vaults outside Obsidian, and I’m completely fine with that.