At least on Windows, you should be able to modify the target property of the program’s shortcut to add any desired flags. Then use that shortcut to launch, or drop it in the startup folder.
On Linux idk, maybe an alias?
What shortcut though? Auto-launch is automatically set by Chrome in the registry, and Chrome really doesn't like you to mess with things it manages in general, and would eventually overwrite this in any case. Also I _think_ messing with shortcuts sometimes has weird effects with Chrome, like on taskbar grouping, though it's been a while since I've tried.