PeroK said:
From a brief look through the relevant chapter I would say that K&K derive the work-energy theorem for a point particle only. And do not generalise it to a system of particles - not that I can see.
The end of the chapter includes a discussion of conservation of energy more generally.
I also found this, which refers to a generalisation to a system of particles (Morin) and includes the additional terms for internal energy:
https://physics.stackexchange.com/questions/247303/work-energy-theorem-for-a-system
I also had a look through Morin (and that PSE link) and generally like how he sets the topic out. The only wrinkle is this annoying internal non-conservative work term which I don't seem to know how to get rid of. Even if I take the system to be completely isolated, I can write the change in total potential and kinetic energy as so (taking into account all interactions, microscopic and macroscopic, so no internal-mechanical distinctions yet),
##W_{int, c} + W_{int, nc} = \Delta T \implies \Delta U + \Delta T = W_{int,nc}##
However, we know that for such an isolated system, ##\Delta U + \Delta T = \Delta E## should be zero no matter what, since it is ridiculous to suggest that the system can be gaining energy from internal actions. So the only conclusion is that ##W_{int, nc} = 0##.
Then, I though we could impose an arbitrary classification into macroscopic and microscopic terms in order to setup the "internal energy" term,
##W_{int, nc, mac} + W_{int, nc, mic} + W_{int, c, mac} + W_{int, c, mic} = \Delta T_{mic} + \Delta T_{mac}##
This leads to
##W_{int, nc, mac} + W_{int, nc, mic} = \Delta T + \Delta U + \Delta E_{th} = \Delta E_{mech} + \Delta E_{th}##
However this doesn't seem to help me that much, since really internal non-conservative forces should be responsible for transfers
between ##E_{mech} \leftrightarrow E_{th}##.
This would suggest a relationship like ##\Delta E_{th} = -\Delta E_{mech}##, which is induced by internal non-conservative forces. However, in such a way that ##W_{int, nc} = 0##. This is completely confusing.
I've been playing around for a day or so but wonder if I'm wasting my time. Every undergrad textbook I've consulted on the matter (e.g. Halliday/Resnick) state that mechanical energy of an isolated system is conserved in the absence of internal non-conservative forces, whilst total energy of an isolated system is conserved regardless. I wonder if this just needs to be taken as an empirical fact, since I'm at a loss on how to derive it!