Why should my choise of OS have to matter?
The Linux question does not matter. But it would have, if you had intended to write to that file.
On Windows, the default install location is C:\lazarus => and any user on Windows can write to that.
On Linux install is in /usr/.... and users can't write to it.
Still remains the fact that FPDoc wants to write something where it shouldn't be writing, at least I guess. If that is the case on Windows I don't know yet. I will let you know if I use Windows at some time when I unavoidable need it again.
FpDoc could probably be improved.
From memory: If you make changes to the content in the FpDoc window, then they will be saved automatically. (And that can be triggered by anything, just moving the caret, or ....)
That part is correct (though could be extended, to allow switching auto-save on/off).
The fact that it autosaves, when nothing was changed... That can be considered anywhere between inconvenience and bug.
And the error message could probably be more informative. I.e. point out that it is caused by the FpDoc Editor.