I think they can, the ECU has a map on the chip, so a different chip can be fitted, it cant be flashed though as far as i know, so its a solder in jobby.
one small problem with the logic you have just said nearly all tdis that i know of that are in the mk3s all run the same ecu which controsl a mechanical pump which has an electronic head put o and the ecu that they use is not one that is chippable unless you solder an eprom in then get that flash mapped, only problem with this is it has minimal mapping possiblities and no one i can find will do it in the uk and trust me iv looked the only place is america, i know all this as im doing my uni project on it and thats why iv gone for a hybrid mechanical tdi conversion with a 12mm head in allowing over 250 horse
We can chip tune the mk3 TDI ecus, power gains will be around 25bhp30lbft. The ECU will need a new set of chips for the software to be loaded on to.The price for the chips and remap software will be £200 fitted.Nick