I am not sure if , at the moment , there is a better way to program ESP32 chips directly using USB without going through ESP-Prog board.
The ESP32 has a bootloader and is programmed over serial. The catch is that you need DTR and RTS pins to load new firmware. Most USB serial cables dont have these pins broken out. I think your options are to put a usbserial chip like the FTDI on the board, or have it external, like the ESP-PROG.
Eventually it will be possible to update the firmware OTA, via WiFi or bluetooth. The ESP-PROG will only be for unbricking or debugging.