The thing is, is I don't remember it reporting the wrong space being used when I first got the phone. I think this started showing incorrectly in one of the two updates we've had since release.
This has not changed as it's been this way since day 1.
Also,It is not reporting out the wrong storage space. You are using 99.5GB of 1024GB(1TB). That is the all in storage number regardless of what makes it up i.e. system, media, other etc.
When you look at the analysis chart, it displays the all in number as a percentage of space being used. In addition to that there is a breakout chart below displaying what makes up the percentage. Notice in the screenshots you provided the 'other' section shows 97GB (not 99.5) because the remaining categories makeup the difference which together come to 99.5GB.
Maybe I completely missed your point but I do not see anything that needs to be 'fixed' as I do not see anything that is incorrect.