Next to everything else that might go wrong with a bicycle on an extended ride, a flat is a relatively minor issue that can be easily repaired trailside, if the right tools are at hand. If they aren’t, a quick fix can turn into a long walk. Well-prepared riders will perform a tune-up regularly and clean their bikes after every ride. For the less-diligent, a well-stocked repair kit will suffice.
We focused on tools that would be useful to a commuter—someone trying to use a bike as a functional way to get around town, as opposed to riding recreationally (road biking and mountain biking). That said, it’s a wild and wooly bicycling world out there, and the streets are packed with so many different bikes, all shapes and sizes, new and old. Customizing your flat-fixing kit has advantages over buying a preassembled kit that always contains a tool (or two or three) that’s a piece of junk, or you don’t need. Or it’s missing something you do need. If you build your own kit, at least you know everything works. And you can add only what’s necessary for your specific bike without ending up with stuff you don’t need.
As you mentioned, it is surprising how often you can get multiple flat tires on while riding, particularly on longer sprints. The tip about bringing a patch kit in your bike repair kit can be incredibly helpful if you’ve already had one flat tire. I agree that all you listed seems like an awful lot to carry, but it’s always better to be safe than sorry, isn’t it?
Friction gear systems are a lot simpler to adjust, because the movement of the derailer cable can be modulated as you ride, every time you change the gear- they require less cycle maintenance. Modern index shifting systems are a little more complicated because each ‘click’ must release the exact right amount of cable to allow the derailer to move the correct distance to move the chain from one gear to another. Setting up and adjusting a derailer is not difficult and requires only basic tools, but there is a methodical procedure to follow.