Wouter,
Adding a Preferences item is not justified in this case in my opinion. The functionality you are requesting is already available through command-line arguments, and a set of process icons can be loaded easily through Process > Process Icons > Load Process Icons. As you already have pointed out, modifying the startup script file is another option that automates this—just remember to make a backup of your custom startup file and reinsert your commands after installing a new version.
IMO, loading a project automatically at startup is not necessary, and is not something I would recommend. Each image processing work is different and should be analyzed from scratch. Depending on a preconfigured set of process icons is not a good idea in general.