I found out some interesting information which is related to this issue.

I wanted to silently autostart flatpaks on my image.

xdg-autostart seemed to work fine, except some apps failed because they require active internet connection.
Intel internet driver can be quite buggy in my case, so it can happen that it starts a bit later or I have to replug ethernet cable.

When I looked into solutions, I stumbled upon this systemd template:
https://gitlab.com/-/snippets/3669472#flatpak-apps

Initially, it didn't work.

I DM-ed the author on Discord & he kindly helped me debugging the issue.

He uses KDE & it works fine on his image.

It turns out that Gnome handles things differently & that WantedBy=xdg-desktop-autostart.target is not working there.

systemctl --user list-dependencies xdg-desktop-autostart.target lists that nothing has started, but EasyEffects clearly did when looking in Background apps. On KDE, it lists some started apps.

systemctl --user list-dependencies --reverse xdg-desktop-autostart.target lists also nothing, while on KDE it lists plasma-workspace.target.

To solve this issue, I changed WantedBy to gnome-session.target (graphical-session.target may also work, but this one is safer, as it starts later).

Additionally having Wants=gnome-session-initialized.target & After=gnome-session-initialized.target also helps.

Reddit post which also helped me:
https://www.reddit.com/r/Ubuntu/comments/15t88ti/using_systemd_instead_of_startup_applications/

module idea: boot-script #119

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