No, Gotek, is a floppy drive emulator only. It can not store data in the way you want.
As mentioned. The ADF files are size limited to the size of a floppy disk.
As for backing up. Then I use windows and WinImage32. Basically anything that can take a raw image of the SD or CF.
Another way is to setup another IDE or SCSI SD or CF card reader and copy using DOPus or Amiga DOS copy. To another partition. I do this as well for speed.