Actually the usercount gets incremented in pose mode by doing anything action there ( move, scale, selection, rotate ), and note that COW is now default. If you play a bit with the file, just select some bones, rotate, scale, .... and do some undo in the middle, Blender will crash and sometimes not able to open the file anymore(crash on start).

I made this quick patch to show if Blender is running with or without COW enabled as I kept getting confused with multiple Blenders while testing.
It has an include for depsgraph, so double check your includes if editing that file.

@Sybren A. Stüvel (sybren) Didn't note the exact revision, but it one from was Monday (14 May) afternoon, (from around 4-5:30pm). I should probably run it again (maybe daily) to check if things have changed with the DM/modifier cleanups since.

Profiling suggests that the main costs are still just modifier evaluation (> 60%)

Regarding PyController Removal + Drivers/Custom Properties Creation Script thing , even though the rig works without it, I realized that the animations in 2.79 are keying these api defined properties, so I should add the script with the drivers trick anyway so that animations work properly.