96 Alternator on an 01 PnP Pro
 

I'm starting to plan the wiring for my prepared autocross only car, so here's my first noob question. I want to get the starting, charging, and power distribution sorted out first. I've read all the VVT swap info and the question isn't really addressed for my situation..
Setup:
01 VVT Engine & 01 factory engine harness
96 Chassis
ECU will be MS PNP Pro MM0105 (2001-2005)

I have both the 01 and 96 alternators. I'd like to run the 96 alternator to keep the chassis wiring changes to a minimum. This choice will of course leave the alternator control connections on the MS at T4 & 3M unused and open.
Will leaving alternator control at the ECU disconnected cause any issues?
If not, is there any advantage to making the necessary changes and running the 01 alternator?

just turn off the function in software.

Ahhhh! So I'll have a function function in Tuner Studio that disables the alternator control. Makes sense. When the 96 alternator fails I'll want to switch to a light weight race alternator, so skiping the use of ECU alternator control makes sense for me. Much simpler swap when the time comes.
Like I said, noob question.

I can't disagree with this decision more. Use the 01 alternator, and then you can chose your running voltage for various conditions, including configurable over charge during overrun and shut off at WOT.

Good points Ben, thanks. I'll probably be running a big ass battery on the passenger floor and shutoff at WOT would be a nice feature to have. I'll take another look at the schematics and see what it will take to make it work.