First off, file access is mediated via software on the Android side. What you are seeing is a database representation of the device FS. And this database can be incorrect (people have in the past deleted folders they thought were empty only to lose files) or used to implement DRM.
Second, it is bloody slow.
The one benefit of MTP is that Android do not have to unmount the FS you are trying to access.
For the longest time MTP & Linux was terribly painful, verging on unusable, while mass storage worked perfectly. It bit when I upgraded my Nexus phone and discovered I couldn't get to the files stored on it.
Fortunately, all seems to work well now.
But oh my goodness! MTP support on Linux was terrible for a while, and even on Windows it wasn't fast and reliable. It was easier at the time to just use a service like Dropbox to transfer files to/from the phone, than to use USB.