Very nice post, thank you! I just finished Ahrens' book and I'm starting a slip box of my own. I really like the idea of a physical slip box, but the appeal of digital apps is strong...
For digital, the main pros appear to be search, tags, graph views, external linking to sites/tweets/etc, and easy bi-directional linking. For physical, there's the research that handwriting helps with information retention, and seeing where the "clusters" of notes are, as well as being able to take them out and arrange them on a desk for a project.
The main thing that seems to be lost in the digital version, to my mind, is "stumbling upon" notes as you flick through certain sections. It seems like you can go "exploring" easier in the physical version, whereas the digital apps I've seen focus more on digital search. I'd almost prefer if an app had a "read next" button so I could flick through them.
There are some points here that are tried and true wisdom, passed down through the great tomes on writing, such as how to cut the fat. I especially like your thought experiment angle for coming up with ideas. I might give that a shot soon!
There are also a few points I'd be inclined to tell a new writer to take with a grain of salt. Limiting oneself to absolutes may damage credibility. “The best history books are autobiographies” is a highly subjective statement, and I’d challenge it. In this way, one can aim for “concrete” and land on shaky ground.
Writing precisely what you don't know is great for one particular style, i.e. the "this is what I learned today" style of blogging. And it can be great for staving off your boredom, but there's also the reader to consider. Some subjects and styles - and especially if the authoritative tone you call for is used - demand a writer who really knows their subject. A veteran who has seen it all and can comment on the history of things. Of course even that writer at the frontier of their field should always continue learning, both forwards and sideways to combine their knowledge with adjacent fields.
I'm largely with you in terms of Getting To The Point, though again, this is about style and subject matter. Nonfiction can entertain as well as inform or persuade, and as long as the reader is engaged, going on a few fulfilling detours can be fun/humorous/insightful. Some of the best stuff barely even has a point, or the point might be elusive (Hunter S. Thompson, Charles Bukowski). Intro paragraphs/sections from new writers can often fail to hook, but there's a place for flowery prose and humour in nonfiction.