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A professional ROM tune IS an acceptable alternative to a standalone ECU, but usually it will be a ROM tune for a recomended mod-set. Any modifying you do to the engine all the way from a cold-air-intake to an entire head swap changes how it operates, and thus changes the way the ECU operates. You must remember that when you slap new injectors into your motor, the computer doesn't go: "Oh, look, new injectors" all it sees is different resistances than its used to seeing and it compensates for that.
That works alright for a lot of different kinds of mods, but once you start getting into extensive engine and fuel system modification it is a good idea to go with a standalone and have the car tuned professionally by a certified EFI tuner on a dyno.
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