We haven't measured this yet, so I can't give you a real answer. Most of the copies we've seen are really mild and don't remove all that much light, so we recommend dimming your screen all the way at night. This will go a long way to help (on top of any intervention).
I don't understand why you say "plugin", it's an advanced android permission only toggleable with ADB (android.permission.WRITE_SECURE_SETTINGS).
If I have correctly understood, f.lux works by removing blue not adding an overlay. If Settings app doesn't use an overlay for color inversion/color gamut / Daltonian colors,
it might either use WRITE_SECURE_SETTINGS or have a "system app" special access to do that. But I would lean on the latter :-/
just upgraded to android 6.0.1, rooted and tested to no avail. still waiting impatiently for android version.
aside from android, i used f.lux on CRT, LCD and two model of laptops. it works wonders on CRT and LED displays, unfortunately LCD (Samsung 740N 17" display) view is awful, nothing near eye comforting. view angle is affected, colors changed beyond recognition, etc. i think LCD technology is not that good to even consider tempering with but f.lux developers can focus on more common platforms like LED and AMOLED perhaps.