Yeah, that's pretty much it in a nutshell. Recuva won't work since it doesn't have access to the filesystem directly (the phone is simply translating the filesystem to the computer in MTP).
Also, since I believe the Nexus uses the more Linux friendly ext3 filesystem (as opposed to FAT32, which flash drives and SD cards use), it actually more difficult to recover the deleted information because of the way the files are deleted.