Looking into it more:
Many of the prototypes in question aren't even touched by my mods, or Icon Badges.
First line of current.log :
0.001 Program arguments: "c:\Users\sandy\Desktop\modding\bin\x64\factorio.exe" "--mod-directory" "c:/Users/sandy/Desktop/modding/mods/" "--instrument-mod" "debugadapter" "--enable-unsafe-lua-debug-api" "--check-unused-prototype-data"
I'll just turn that off and move on. Nothing to see here. I just won't be able to check for any of my own unused prototype data.