Gotek drives can have several firmwares. I have a Gotek drive equipped with HxC firmware. I use it on Amiga hardware to read *.adf and *.st files directly from USB sticks, it just works fine (including with EmuTOS for Amiga). However, I never tried it on Atari hardware. It should just work equally well after proper configuration, there are many settings.
If your Gotek is not equipped with HxC firmware, you can buy that firmware for 10 € on the HxC store
. Then you can find free updates on the main HxC page
(look for "USB Stick STM32 HxC Floppy Emulator").
If you have any question regarding to the HxC firmware, you can ask on the HxC forum