I solved this myself.
The solution is #2 (using tkg-tools from github), under Windows. For some reason the board wasn't recognized by the Linux machine (Now that I'm thinking about it, maybe I need to recompile hid_bootloader_cli from source) but it was recognized under Windows. When I first tried under Windows, the antivirus software blocked hid_bootloader_cli.exe, but when I disabled the antivirus software temporarily, the flashing worked.
For future reference for anyone having trouble with Daisy PCB, I hope this helps!