Why wiping "Data" in recovery doesn't wipes my Media in Internal SD card?
Well this sdcard thingy is kind of tricky for the OPO. For me it seems like the device does not have an sdcard at all(not even an internal). Which would mean that the free space you see is actually an emulated internal sdcard taken from your device flash memory. 

For emulating an sdcard a FUSE daemon is used where also your /dev/fuse device comes into play. This is probably the raw presentation of your flash memory made accessable via your kernel. Which is then mounted to /mnt/shell/emulated.

Additional Info about FUSE: http://en.wikipedia.org/wiki/Filesystem_in_Userspace#Virtual_file_system.

To back my assumptions about the emulated internal storage see the storage configuration file for the OPO: 
https://github.com/evolve-bacon/android_device_oneplus_bacon/blob/lollipop-5.1/overlay/frameworks/base/core/res/res/xml/storage_list.xml

Now to your question why your /data/media directory is not wiped while doing a factory reset:

This is just a nice feature when there is no physical external sdcard(or even internal) present. So that you don't loose your important userdata like downloads pictures etc with a data wipe.

What Cyanogenmod did here was declaring an external sdcard on your emulated internal sdcard which resides in /data/media.

For full understanding see: https://github.com/TheOldUnas/Bacon-Lollipop-Boot/blob/master/boot/ramdisk/init.bacon.rc

Especially the declaration of: export EXTERNAL_STORAGE /storage/emulated/legacy and the FUSE daemon for /data/media: service sdcard /system/bin/sdcard -u 1023 -g 1023 -l /data/media /mnt/shell/emulated

For final understanding compare on youe device the output between ls -l /data/media/0  and ls -l /storage/emulated/legacy and finally ls -l /sdcard. It is all the same as it is your from emulation, emulated external sdcard :D

For your comparsion between fastboot erase and data wipe through android/recovery. Fastboot is part of the bootloader and does not know about all this emulation mess so it will completely wipe data.