I use Obsidian, installed only from the Manjaro repository - not from the AUR, and not Flatpak or any other containerised system.
Where any package is available in the Manjaro repository, this should be the natural choice to avoid the complications and potential conflicts introduced by other methods.
sudo pacman -S obsidian
Using Obsidian from the Manjaro repositories allows it to be updated as expected when you run the usual update command:
sudo pacman -Syu
You seem to be a little confused.
Nothing is ‘installed through Electron’ - Electron is a actually a dependency of many applications - including Obsidian. Those applications are built using Electron as a basis; an Electron package is installed for all Electron-based applications that you might happen to install. Obsidian is only one example.
These are packages usually installed along with Obsidian:
[nix@nix ~]$sudo pacman -S obsidian
[sudo] password for nix:
resolving dependencies...
looking for conflicting packages...
Packages (15) adwaita-cursors-46.0-1 adwaita-icon-theme-46.0-1
at-spi2-core-2.52.0-1 desktop-file-utils-0.27-1
electron28-28.3.1-2 gtk-update-icon-cache-1:4.14.4-1
gtk3-1:3.24.41-1 iso-codes-4.16.0-1 libcloudproviders-0.3.6-1
libcolord-1.4.7-2 libei-1.2.1-1 libepoxy-1.5.10-2
libxinerama-1.1.5-1 tracker3-3.7.3-1 obsidian-1.5.12-1
Total Download Size: 86.88 MiB
Total Installed Size: 346.53 MiB
:: Proceed with installation? [Y/n]
All of these packages are installed to support Obsidian. Many of these may already be installed to support other apps you have installed.
If installing Obsidian as a flatpak it already contains all of those dependencies even if you already have them - so, the apparent convenience of flatpak comes with undesired overhead - in the form of wasted space.
There are also other reasons to avoid containerised apps (flatpak, appimage, snap); but I’ll leave that for others to mention, as the topic can get quite involved.
The AUR should be avoided - point blank - unless there is absolutely no other alternative. Remember, the AUR is not officially supported by Manjaro.
This means that if something installed from AUR breaks your system, it’s your responsibility; Manjaro will not magically fix it for you. That said, forum members might have a suggestion or two, regardless.
Using the Manjaro repository version of any package just makes better sense. All you need do is update regularly; and this is already expected of anyone using an Arch-based rolling-release distribution.
Sometimes a package might not exist in the Manjaro repositories. It is only in that circumstance that any other method should even be considered.
I hope this helps. Cheers.