Normally you'd use sleep modes instead of actually powering the device off. You could control sleep using a button and firmware if you wanted to have user control.
There is also shipping mode, which basically disconnects the battery. The problem is that the only way to get out of shipping mode is to power the device externally using USB or VIN.
The EN pin on the power module controls the 3V3 output. And the 3V3 output controls the VCC (3V8) output. However you can't control that from the MCU because when 3V3 is turned off, the MCU would not longer be powered, and the pin would revert to Hi-Z and the pull-up would turn the power back on again. You could connect EN to a physical switch, however, the Muon does not expose this pin on the expansion connector, because we really do not recommend abruptly removing power under user control without gracefully shutting down the system first.
However, what is the use case for needing a power switch? For developers, you just unplug the USB. If you're building a product, you typically only have one power source, so being able to turn off every power source is rarely required.