To address the concern in the topic title - this is normal with Manjaro.
Mirrors update at different intervals - and because when pamac-mirrorlist.timer is run it will generate a random mirrorpool of 8 up-to-date mirrors.
$ cat /usr/lib/systemd/system/pamac-mirrorlist.service
[Unit]
Description=Generate mirrorlist
Wants=network-online.target
After=network-online.target
[Service]
Type=oneshot
ExecStart=/usr/bin/pacman-mirrors -f8
ExecStartPost=-/usr/bin/pacman-mirrors --status
Due to the randomization the mirror pool will be different across systems.
If you really want to ensure they are as close to identical as possible ensure you are using a single mirror which is provides sync in a stable manner.
You can use the interactive functionality of pacman-mirrors to create a custom mirror pool containing a the single mirror you have found to suit your usecase.
Depending on your location which one to use will differ.
If I use an external mirror - as opposed to my own - I prefer the mirror provided by [easyname.at]
sudo pacman-mirrors --country at --interactive
Then select only the easyname mirror and save the mirror pool
Repeat for any other system you have.
As for AUR - you know it is unsupported - so there is that.
Please consider alternative ways to check for update to custom scripts. Pamac is using a CDN distributed copy of a database generated by aurweb team - the database may or may not be up-to-date - I really don’t know.
What I know is working → [root tip] [HowTo] Check if your AUR build scripts have been updated