It boils down to this, any workout you do, you really have to do it properly. As well as, like you said, in moderation. Any reputable physical trainer or therapist will tell you that recovery days are critical. (And if a physical trainer tells you that you can do all this weightlifting or distance running without recovery days, then that's your clue that they are probably not reputable.)
I've found that when most people think of long distance running they focus on pushing themselves, but in practice I've found that a huge part of the sport is avoiding and properly managing injuries. It's a bizarre sport because getting injured is an essential part of it.
Myself and many of my running friends have started working more frequently with PTs and I've personally found it really, really helps identify and fixing the real cause of injury. But it sounds like you have much more experience then me so I am genuinely curious if you made heavy use of PT and still succumbed to chronic injury.
In my experience, the most important thing is to make sure you build up the amount of running (quality and quantity) in a proper progression (don't do too much mileage or too much speedwork too fast).
"Overuse" injuries are quite common, though. They're injuries that you get from doing more than your body is capable of at the time (often just trying to do "too much too soon"). These injuries go away when you reduce the stress on your body. They can last a long time if you continue to overstress your body by running too much (or failing to fix problems in your running form, which is a form of that), but they are not what most people would think of as "chronic" injuries (that stick with you indefinitely). You have ongoing overuse injuries only if you continually run more than your body can handle.
I would also add that just because you get an overuse injury at, say, 40 miles/week of training doesn't mean you can never run more than that injury free. You need to reduce stress, run less, let your body strengthen (or fix running form problems) and then slowly increase training again. Years ago I had issues when building average miles up over around 30 miles/week. They took some time to work through. Now I run average 50+ mile weeks for most of the year and I'm perfectly fine (actually feel much stronger and in better health than before). I need to be careful during periods when I'm ramping up to 80+ miles/week for an upcoming race, increasing stress on my body. Running injury free can require a lot of problem solving.
As an aside, I did run down at the Caballo Blanco race with the Tarahumara down in the Copper Canyons last March. They changed the course this year and made it a lot more "technical" (more trail running with lots of rocks). The winner of the race, Miguel Lara, wore running shoes, not huarache sandals. He has won many times before wearing huaraches, but chose to switch to shoes this year because of the increased technicality (primarily rocks) of the course.
Virtually every non-runner I know, whenever I mention something about running or racing, tells me they "can't/don't want to run" because it will "destroy their knees" when in fact runners have stronger knees than non-runners [1].
It'd be if you were a weakling and said, "I don't want to lift weights because that will destroy my joints." If you lifted weights too heavy too soon, yes, but the way to getting stronger is through slow progression. Which people don't want to do.
It's just a matter of consistency and steady effort. Beginnners always rave to me about their 17-20 mile long runs when my question is "How many miles per week have you run? And for how many weeks in a row?"
The Five Fingers stuff, glad that works for a small segment of people (I even own a pair) but for most it's just going to end in stress fractures.
[1] https://www.runnersworld.com/news/a20804690/runners-have-muc...
Final revelations came when I discovered how many people I knew were on steroids (to heal fast) and painkillers, all amateur runners and cyclists.