I tried using AT commands, but I can only control some aspects of the phone, I cannot flash the phone with AT commands.
The conclusion: I didn't find any way to flash the firmware in Linux.
But I found some interesting things you can do: fully use the AT commands to make calls, backup you agenda, write/receive sms from the PC, synchronize calendar, etc.
You can even use the phone as a remote control through the bluetooth.
I will create another thread with all the cool things one could do with Linux and a Sony-Ericsson phone.
The thread is: Interacting with your phone in Linux