Okay, I'll be serious!
I do agree with the implication that all these considerations are just members of the large family of self-imposed distractions and, at the base, excuses. What matters is the writing, the result, as you said. But still, as someone who just decided to tackle a first novel, I appreciate the convenience of Scrivener insofar that I don't get burdened with aspects like organization. It handles all that, so I have fewer excuses to monkey around or get lost in irrelevant details. From that perspective, the chosen tool increases productivity and leads to "more" result.
We could probably write our stuff on toilet paper, too, and at least I would get the same results, but if fundamentally unimportant details (like the software environment) make it easier, why not?