Some years ago, I used to live on my bike. Riding around daily through any weather condition was bound to quickly wear down on the bike over time. I like some of the stuff that you have in your toolkit. I would say zip ties are actually really convenient, because when something came loose you could go ahead and use those to fasten them down to keep on moving ahead until you had enough time to fix it or get it checked at a bike repair shop.
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.