Hi Kalun.
I have experience on mainly Motec systems, but concepts are still the same.
Re your query regading differing maps for similar engines, I have wondered this too but other than the sizing of injectors, there are a couple of other things to possibly consider too. Firstly, I've seen engines both with and without a manifold referenced fuel pressure regulator which makes a big difference. On a motor with a pipe from inlet plenum to regulator, the fuel pressure is lowered when at idle due to the vacuum and then it increases the fuel pressure at wide open throttle, or even further if the engine is boosted by blower/turbo. The effect of a lower fuel pressure at idle or part throttle means that the FUEL MAP will require larger values to flow the required fuelling. Without the pipe connected, the values will be much smaller as the fuel pressure is then higher, but this can make the injectors difficult to control as they then need to open for much smaller periods so resolution of adjustment can be lost. At wide open throttle, the MAPS will look the same with or without the reference pipe.
There is likely to be a clear difference between maps for 4/8 throttle setups. The throttle position is normally a voltage that represents the angular position of the choke plate within the inlet passage. If both throttle types were set to a position representing 50% throttle (say 2.5v), then I would think the air flow available to an individual cylinder is going to be different for each motor/throttle type combination (4/8 barrell). Hence each FUEL MAP will have a different value at the same throttle position to give the correct fuelling for the different airflow.
Thus - if you mapped for a 4-barrell on a motor, then removed it and fitted an 8-Barrell setup, the MAPs would be quite different. All down to differing flowrates at similiar throttle positions...
Re-reading I hope I've not clouded the issue, but either way it's my 2c...
ps - I use a Motec Wideband Pro Meter which integrates easily with the Motec ECUs or can work standalone for other systems. Working alone it does not have any logging capability though which can help a LOT for on the road tuning, esp if you're on your own - Therefore I'll be adding one of these to my kit soon. (Both systems will be available for loan/hire to UK users)
LM-1 Wideband O2 Digital Air/ Fuel Ratio Meter | Lambda Sensor Controller