huh? TFTs are for returning to stock ROM and/or kernel and baseband, custom ROMs come in ZIP files which are flashable in recovery. What I do is download the ROM zip on my phone and flash it straight after via recovery, no need for a computer at all.
FTF's are not just for returning to stock, not at all, they're used to flash rom's too as the kernel and baseband needs to be flashed also.
Check out monx's thread, the instructions for install states to flash the rom and then without allowing a reboot, flash kernel and system (afaik)
Simply flashing the rom wouldn't be enough without flashing those files via flashtool.
What i'm trying to ascertain is do I have to do this every time as it's a pain in the backside.
Quote from Monx
LOCKED & UNLOCKED BOOTLOADER
BACKUP any critical data to microSD
Copy this rom zip package to microSD
Reboot in recovery, (do nandroid backup), do factory reset & install rom until finish
IGNORE RECOVERY INSTALLATION WARNING. SELECT NO & PROCEED AT THE END OF RECOVERY IF USING CWM RECOVERY
Skip (x) steps if u already running same base firmware with latest monxDIFIED base rom. Else, proceed.
(x) Turn off device. (Hold power button + vol up until vibrates 3 times) [or use recovery turn off device option, if any]
(x) Flash latest Sony's firmware (FTF) matching current latest monxDIFIED base rom using latest flashtools. UNCKECK all WIPE options and CHECK only SYSTEM & TA in EXCLUDE options.
(x) Disconnect USB cable & turn on phone. Done.