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When I plug in my Android device to my computer it gets connected as a media device under MTP mode. I can browse a bit of the folders on my device via my computer. I'm wondering how much of the device am I actually able to see? What sort of folders and content specifically is not visible over MTP? Does MTP have a corresponding set of file permissions associated with it?

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MTP - an extension to PTP - is a client-server protocol, roughly like FTP. MTP client on PC sends operation requests (like GET_OBJECT, SEND_OBJECT, DELETE_OBJECT) to server running on Android device and gets responses back.

Unlike USB Mass Storage (UMS), MTP doesn't expose filesystem at all. Instead contents of shared external storage (/sdcard - a subdirectory of /data/media/ - and physically external SD card) which are indexed in database of MediaStore Content Provider are shown to PC. Everything else (including /data, /system, /vendor and other filesystems) is not visible over MTP.

Since there's no filesystem level access, there're no filesystem permissions. Related details:

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