Popcap is just one of the ways to design an RTS, there are others.
Zero-K solves the problems solved by popcap in other ways. Income tracks map control, and controlling more of the map is hard, so players that are ahead don't have the freedom to sit back and build up an overwhelming army. Armies are fighting or jockeying for position throughout the game and army size and composition keeps escalating. Defenders advantage shifts to attackers advantage as things escalate, so people can't just sit in their base. The overall effect is that, while there is a pop cap at the technical level, it is 10x higher than the unit counts that even the largest battles tend to equilibrate to.
Talking about the lack of popcap is a bit backwards in a way. There are just so many subtle things that mean the question of popcap never has to come up. Maps are pretty open, units don't fire through each other, AoE exists... the list goes on. A better question might be why games with a popcap couldn't be designed away from the failure mode of people sitting in their base making larger and larger armies. Having to put a hard cap on army sizes, that people regularly reach, is sort of a drastic measure.
On supply, I'd say what you said about supply is pretty important. But the aspect of it you bring up isn't limited to popcap. Eg C&C games have power plants that act as construction supply. Rebuilding your base is easier the second time around, as long as you keep your power plants. There is something similar in Zero-K with energy. Metal comes from points around the map while energy can be built in your base, and both resources are used for construction. When you take more metal spots you also need more energy, and the energy is nowhere near as vulnerable. That is the main supply-like comeback mechanic, which works since part of your economy is always vulnerable. Reclaiming wrecks for metal is another comeback mechanic.