Why would an STM32 flight controller need programming interfaces other than USB?
You can program firmware via USB just fine, that is not a problem. It is perfectly good for firmware updates.
Why you should have SWD interface is not because of programming the MCU, but debugging the firmware.
It would be pretty anemic to have high performance MCU there, and you are limited to debugging code problems over serial console, LEDs, pushbuttons etc, instead of using a proper tool for that.