Using VBUS instead of the USB port to power a MCU
Applying 3.3V to the regulator input will likely result in an unregulated output of &lt;3.3V (3.1 to 2.7V based on power draw up to 150 mA) Its not a perfect pass through.
And while the regulator accepts up to 10V, you need to consider the voltage rating for anything else in the path, mainly capacitors, or in this case other ICs, or the LEDs. And voltage drop in heat across the linear regulator. A higher VIN leads to a higher wasted heat. If you want to use a 9V then you'll need an additional regulator for 9V to 5V.
If you skip 5V/VBus and apply a regulated 3.3V at the 3.3V input then the device side would be fine, the debug side unused and the 3 leds will not be powered.
Specifically though, you can apply 5V through the USB port without using a computer. It can be with an adapter cable, a USB power supply, or a USB power bank (some have auto-shutdown features which make them annoying to use with low current applications). The USB VBUS connects to the VBUS pin via the power switch. No real electrical difference there.