it looks like you can mod the timing instead of just the fuel curve on that maft pro system- i haven't seen a piggy back also tune the ignition timing before - it looks basically like a daughter board to hook up to the existing ecu that you tune with to mod the existing ecu code but through the maft pro computer. is this correct?

to answer the eprom questions.. meaning if you say remove the batter form your car you loose your data.? no..
to answer how the maftpro works.. (ive only used an safc2 so ill state what i know from that ) it wires directly into the ecu and overrides the date.. telling it to do what you program in. essentially

so its like having a daughter board then like nistune basically?

EPROM is a type of flashable memory (usually with an onboard controller)... no, early Toyota's were not flashable. There were companies who would remove the processor (which had an integrated ROM) and replace it with a programmable daughterboard with flashable memory and another processor... but they're impossible to find and even harder to find support for.

The MAFT Pro doesn't work like a traditional piggyback nor does it work like a traditional daughterboard. The Main processor is still present and still following all of it's routing maps. The MAFT Pro (depending on the setup) wires in both before and after certain systems. Definitively, it is a piggy back... but it's one that's grown far beyond what has been done elsewhere. The overall compatibility of the system and its increasing popularity make it very well supported and you often find that you're able to help or get help from other owners running it on completely different vehicles. However, like any piggyback, it's still reliant on the host system to determine the base values and how to respond to changes whereas with a standalone that one box is it.

Unlike the NisTune the MAFT Pro is a self contained unit with it's own display and keypad. Tuning and datalogging with a laptop is still the way to go.

One more thing to note is that the MKIII does not have a wideband O2 sensor... it's Lambda. The MAFT Pro can integrate with a wideband (such as the Innovate Motorsports LC-1) for on-board tuning and also to monitor and automatically adjust for a specified AFR at WOT (very nice!) and idle and cruise if the ECU is placed into full time open loop mode.

The MAFT Pro can also be used to modulate the TPS signal or as a TPS/RPS switch (again, ofter very handy).

Now, like all other piggybacks the system does have its drawbacks as well. There are certain things in the stock ECU with must be bypassed or tuned around and you're bound by the fundamental base code of the stock ECU... including its quirks (like running very rich in open loop operation when that car is started warm versus after a cold start... there are ways around this but the existence of this bug pisses me off).