From what I've searched so far I didn't found a native application (native to Linux) that would flash the phone.
I tested Setool Lite through Wine in Linux and it worked, but I cannot use properly the DCU-60 USB cable. In Linux all the drivers are embedded in the kernel, and I cannot install Windows drivers in Wine, Wine just uses all the devices that the kernel recognizes. The Linux kernel interacts with the phone just as an external storage device and as a modem (AT commands), the S-E drivers or any other third-party drivers are usable just on Windows. So, the trick (Pressing C and connecting the cable) does not work in Linux because the Linux kernel doesn't support this.
The conclusion: So far, I didn't find any way to flash the firmware in Linux