It also messes up the way the ECU handles the fuelling...
It doesn't just remove the cut, it shifts the fuel cut, by shifting the boost values the ECU reads.
Say for argument sake:
1V - 4 PSI
2V - 8 PSI
3V - 10PSI
The FCD (if it is an HKS type) will make it:
1V - 3PSI
2V - 7PSI
3V - 9PSI
4V - 11PSI
So if say the ECU usually cuts of at 4V, 4V will be equivilant to 11PSI. However the ECU will still see the wrong values, i.e. at 2V it is really 8PSI and not 7PSI, so the ECU will fuel for 7 PSI when you need fuelling for 8 PSI. Hence the whole need of fuel regulators and such things.