Comment 4 for bug 1517262

The file is indeed written as far as I have been able to check. This, though, makes the system-wide setting a bit confusing.
Unless, of course, you want to allow the system administrator to enforce the start of the program for all users due to its privileged nature.
If so, still, especially in order to provide (visual) feedback to the logged user, the startup option should appear checked.
The user-wide file be created too? In my humble opinion, no. At least not as it works right now.
I would create it as a sort of 'non autostart setting' if you want to keep the system-wide one at all cost but allow a user-wide setting to override it. This would also avoid the redundancy of 'autostart files', especially the user-wide one.

In my humble opinion and if no 'enforcement' idea is on your mind, that should do the trick.
Even though, on my behalf, I like the 'only user-wide setting' approach more than dealing with a single, system-wide and privileged file.

My .02 cents.