I'm genuinely interested in knowing what these legit ways are.
The only one I can think about is that you (not you but the user) underestimated the time the guide would take (even though that was understandable when it took 11 hours but isn't so relevant now that 1 hour is enough) and you "have to" go to bed right now right when your N3DS was on 2.1, and you kind of unconsciously close it before thinking "owait the guide told me not to".
In that case, maybe the guide should add time estimation for steps and specify where it's safe to take a break and where it's not (like have a red background where it's not)?
Other cases I can think of are indeed you (still not you) not taking care of your stuff so you don't even deserve a unhacked 3DS. That's why the 2DS was created.