My guess is that to a casual driver the difference having it open or blocked off wouldn't be noticeable. To you on the track, you could choose which way is more advantageous.
Normal function is closed below 3k rpm, open up to 5k, then closed again; so, best low and high end power = closed, best mid-range = open.
Check this old post. The .PDF link in it is dead now, but I had quoted the important part:
What's the function of this valve?
Running with the 1997 DME could also be an important factor. Probably closed (less high velocity air) will be best.
I have a 2001 2.7L DME/Immo/Key set boxed up. I could send it on loan if you want to experiment. I should have an e-gas pedal too and could dig it up along with the connector and some of the wire to the DME.
The other variable might be injectors. I noticed that the injectors I swapped from the 2.7L were a different color than the ones that came off the 2.5L. They may be different pressure and factor if you are running too lean or rich. I don't know the specs....
So... quick and simplest configuration to try: block the second tube and adapt your cable throttle body to work and use your 2.5L engine harness. If that isn't good, it's a starting point to work from.