There are a few different ways to steep grains. I think you can do either of the above, but I bring the water to something below boiling, the add the grain bag and hold for 20-30 minutes. I measure the steeping temp.
The kit uses hopped extract, which is why it calls for a short boil. I would lean toward following directions. Keeping light color isn't an issue for a stout. It's not a 60 minute boil, and I don't think you have to worry about IBUs due to boil gravity. The bittering hops are already in the extract.