Bluefruit EZ-link is described as programmer. It means it supports RTS/DTR:
The EZ-Link has another impressive feature: the DTR/RTS/DSR flow control pins are automatically synced to the computer serial port. What this means is that if the computer sets the hardware flow control DTR or RTS pins high or low the pins on the bluetooth module will follow.
So Arduino IDE performs reset to initiate flashing (as Arduino's Bootloader wait for few seconds after reset for upload commands from Arduino IDE). For USB reset works by switching DTR to 1 and 0 and special schematics on Arduino board monitors it and performs reset. After reset is done Arduino IDE runs avrdude and start flashing.
The question is "How does it works over Bluetooth module by Adafruit?" There is no RTS/DTR line for Bluetooth..
PS. I believe virtual COM-port drivers for this Bluetooth device should send special AT+ commands and Bluetooth device should handle them and perform setting 1 or 0 to special pin wired with MCUs reset. But this requires Bluefruit bluetooth driver to be used. But i can't see it requires special BT drivers at computer.
RFCOMM do support flow control. RFCOMM is based on GSM TS 07.10. Bluefruit extract info on RFCOMM and map it to flow control lines.