The Holley gets you timing control, which is a $200 upgrade for Fitech. You will make more power with better timing control than with different fuel injection. Both run a wide band O2, so the air/fuel will both be the same (so long as set up the same way).
FiTech runs the MAP off a single bore. Gets confused when used on a divided plenum intake (typical dual plane intake). Which is why they say run on an open plenum.
Holley uses a branched MAP so it reads both sides of the intake. Doesn't have the open plenum requirement of FiTech.
Holley can get a progressive throttle linkage kit and the software will support it. Something that can matter if you want drivability and not just full throttle performance. Have not seen that for Fitech.
Talking with both reps at SEMA a few years back, Holley impressed me more. I ran a Sniper on a stock(ish) 460 in an F250 for a couple of years. Actual driving, not much of a difference. Cold start, cold drivability, hot restart, all WAY better with EFI. I am sure air/fuel was better controlled, but didn't change the fuel economy (still 10 no matter what you did). Could sit for a month with the controller plugged in and not run the battery down (I hear Fitech has issues with that).
The only down side I had was it wanted a 2½ second pause between key on and engine crank. Give it time to reset the IAC. If you waited, no issues. If not, you had a longer crank time, sometimes. I just learned to key on, put on seatbelt, start and drive away.
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