Which one is better? (long)

Why would you need to cut the floor for an a727 which most of them came with ?
He didn't say he'd need to cut the floor for a 727. He said he didn't want to cut for an A500/518.
Most factory FI cars will throw a code if the gas cap is loose. That indicates a non vented system.
Since he's not running any emission controls, he'll need to get the pcm reflashed anyway. That code will not be valid in that case.
Also if using a factory ecu you may have to add various sensors to your engine as well as O2 sensors.
He already has all the sensors, as he's swapping in a complete '96 5.9.
Aftermarket FI systems are much more user friendly and can be tuned. The factory setup really can't.
I might rethink this before you start to buy things.
The factory PCMs (JTEC- OBDII) can be easily reflashed by any place that has HPTuners software, and other common software suites. The parameters of the factory PCM limit their use in max HP builds, but are easily adaptable for street or street/strip use.