// However I'm still struggling to grasp that there can be a negative energy that would make a hadron weigh less than its components. //
I started with the example of a nucleus, where the binding energy means the nucleus weighs less than the sum of the individual nucleons. It's obviously trickier in the case when there's an individual component that seems to have greater mass than the thing it's in. I still need to think about how to address this aspect without melting my brain, let alone anybody else's, but...
The binding energy inside protons and neutrons is even more of a mess. One particular aspect that confuses me is that some, or perhaps even most, of it is thought to be due to the quarks inside the proton etc flying around at close to the speed of light, and yet barely going anywhere. If you wanted to think about it in terms of something easier to picture, it's helpful to think I guess of gases, where the various gas molecules can be zipping around super-fast, but barely get anywhere before hitting something, so from a distance it looks like the air is still.
This *still* isn't addressing intrinsic charm, and I'm really sorry about that. But, yeah... particle physics is hard, and there's a lot to try and get your head round, and if y'all are patient I'll do my best to answer this and any other questions as best I can.
https://profmattstrassler.com/articles-and-posts/particle-physics-basics/the-structure-of-matter/protons-and-neutrons/