@Lazar-Demin just tried flashing the dock and it worked for one of the docks one of the docks continued to display the error.
For the dock that did work:
I wired the dock as you suggested with 3.3v and GND wired to the dock.
Function SPI MISO -> Mini Dock and Omega Pin 1 -> Arduino Dock Pin 12
Function SPI SCK -> Mini Dock and Omega Pin 6 -> Arduino Dock Pin 13
Function SPI RESET -> Mini Dock and Omega Pin 7 -> Arduino Dock Pin Reset
Function SPI MOSI -> Mini Dock and Omega Pin 19 -> Arduino Dock Pin 11
Function VCC -> Mini Dock and Omega Pin 3.3V -> Arduino Dock Pin 3.3V
Function GND -> Mini Dock and Omega Pin GND -> Arduino Dock Pin GND
Here are some photos of the wiring.
I then powered the minidock which and ran the script on the Omega via ssh terminal.
So for me. One of the Arduino Docks works but but it looks like the other one does accept the bootloader (might be fried.)