Adding an application at Startup is quite easy with Gnome Tweak Tool, but it lacks customization.

The problem I'm facing for now is that I would like to start programs like Empathy or Transmission, but the first without displaying the contact list or any other dialogs on startup (-h, --start-hidden), the second minimized in notification area (-m, --minimimzed).

For now, I have to manually edit the .desktop file added in ~/.config/autostart, but that's not very user friendly.

I don't think either that allowing the user to edit the desktop file from the "Startup Applications" tab is more userfriendly, as it was done with gnome-session-properties (dropped since 3.12), just because all the applications don't use the same arguments and the user would have to search for them.

So, maybe Gnome Tweak Tool could add the ability to select from one of the Desktop Actions mentionned in the .desktop file?

In Transmission GTK, the .desktop file is quite well documented:

[...]
Actions=Pause;Minimize;

[Desktop Action Pause]
Name=Start Transmission with All Torrents Paused
Exec=transmission-gtk --paused 

[Desktop Action Minimize]
Name=Start Transmission Minimized
Exec=transmission-gtk --minimized

So, we could select one of these straight from the Startup Applications tab: Default, Paused, Minimized... And it would "just" need these applications to document with Desktop Actions their possible startup options.