On a 98-04 JTEC/JTEC+ PCM, the throttle position shows up in only a few places in the PCM configuration. Most functions are driven by MAP, but the TPS does drive the switch to wide open throttle, power enrichment and a few other things.
I also have a BBK 62mm, but I've also done mods that really have an effect on power. Roller rockers, tuning with a wideband O2, headers, cat back exhaust and intake. I plan to go much farther on an NA setup where eventually the throttle body will make a difference, but I'm not there currently. As is, my assessment is that the BBK is not causing any issues aside from a bit of whistling, but as was shown by Jezza's bolt on dyno tests, it's giving no torque or hp gained until you start to get well above the horsepower the 4.0L was designed for.
I also agree that it increases the amount of air passing by the valve at part throttle, at a given pedal position.