Pamac can be a great application - but can also increase the complexity of a sync process or as you call it update.
The root of your problem is complexity.
I suggest you do as @cscs suggests - perhaps not the removal of pamac - but instead of using a multi-purpose tool - split the process using the tool designed for that process.
multi-purpose tools is like a swiss army knife - they become cluttered and hard to use …
- system packages from repo
sudo pacman -Syu - custom build scripts - use an AUR helper which can be targeted to rebuild custom scrips only
- flatpak - use flatpak’s own update command
Use AUR to notify when your preferred scripts has been updated or use home brewed script like
Also bear in mind that using AUR always assumes an Arch Linux system - and this may not equal a Manjaro system - unless you are using unstable branch.