Whereas I’m not sure most manjaro users ever use any variant pacman -F 
But I suppose this does bring up some points that have gone unspoken.
Which is more or less that you want to run the things twice.
First you get everything new and changed:
sudo pacman -Syu
sudo pacman -Fy
Then you want to manage your pacnews - specifically pacman.conf.pacnew:
(example using meld and directly)
meld admin:////etc/pacman.conf.pacnew admin:////etc/pacman.conf
Then do it again so everything is lined up:
sudo pacman -Syu
sudo pacman -Fy