Okey, I made some testing my self, I took backup to Mac, and shows same space than iOS:

Then cleared my iPhone totally to factory settings, started phone and uploaded my backup back to phone as big it was before not much space left.
Here what happened after phone reset and loading backup back to phone:

Here is again before reset and backup:

Some reason backup is now smaller than when I made it, so I lost some of that gray iOS area, but I didn't delete anything and all same apps are back and settings.
Also now my system data is larger than before backup, also iOS space is little bigger some reason:

Here is again before when I had less space at phone but System Data was almost nothing:

Here is Mac screen after backup is loaded back in same state:

Maybe some bug and system updates make mess inside data, also backup maybe some reason don't copy all information, or there is error in showing free space, can't say what makes these differences, but maybe something is bugged as after same data and backup is loaded, I get much bigger System Data space readings.
Hope this helps if some one has lot of gray iOS space and want to try clear that, this helped me quite lot.