I don't use WiiFlow, but have seen 2 "boot app" options before, the first is that you can choose a default app or game to start when WiiFlow starts (like with Homebrew Channel) but if this was the case i am sure you would of worked it out. The second is it's an option too auto boot an app when the Wii starts using Priiloader, I find the second to be more likely as I use a similar option to boot straight to the postloader app, so I guess this would set the Wii to boot straight to Wii Flow.
Hope this helps you at least a little.