It depends on which "USB protocol" you're talking about. With USB-C, there are five separate data buses on the plug, each running its own protocol. There is the traditional USB 2.0 bus (half-duplex differential pair), a pair of differential dual simplex buses (normally USB 3.0/3.1/3.2, can also be used for alternate protocols like DisplayPort), a pair of sideband wires (used only by alternate protocols), and the Configuration Channel. All configuration of the other data buses and of the main power bus is done through the Configuration Channel, in simple cases through resistor values, in more complex cases through the USB-PD protocol.
So yeah, you have to speak the "USB protocol" to switch to more than 5V or more than 3A, but the "USB protocol" you have to speak is not the traditional USB 2.0 or USB 3.x protocol, but instead the completely separate USB-PD protocol, which runs on its own dedicated set of wires. I doubt you can show up as a pen drive full of malware through the USB-PD protocol, but I don't doubt that cutting the other buses (keeping only the Configuration Channel/VCONN and the main power bus) will still work to deliver power, even at higher voltages and/or currents.
The reason this isn't standardized (as far as I know, a "charging-only" plug is only allowed as a captive cable on a non-charger) is for compatibility: if your device doesn't understand USB-PD, it might not charge at a full speed unless it sees a short on the USB 2.0 bus (Battery Charging specification), and doing that short on an adapter would allow a device to draw too much power from a non-charger.
I also don't believe any OSes offer a mode where they negotiate power delivery and not data, though I'd love to be wrong - that would be 90% of my proposal. It wouldn't let you authenticate individual devices, but it would let you go back to having a single port that's just a charging port.