I agree that you're overthinking this, but I understand. I do the same thing. My situation is compounded by the fact that I spend my workdays on a Windows PC and my personal time (passion projects) on my MacBook. Therefore, I gravitate toward browser based apps that I can run on either operating system. Craft isn't a bad choice, and the native Mac app is outstanding (the web app a little less so). I mentioned Highland 2 in another comment. It is like a combination of Scrivener and Ulysses, markdown based, but focused on one project at a time, rather than giving you a quick listing of all of your projects. I find it appealing, but since I can't use it at work, where it would do me the most good, I am not using it.