This JUN replica intake if made to spec should flow more air not replacing TVIS. You can gut the TVIS. I did mine and it just act as an adapter plate now without throttle plates which aids better air flow. If you take a careful look at the manifold, TVIS assembly and the head all are misaligned by a couple of mm. You can mark them and grind them to align up the holes, that would give much better flow as steps causes air turbulence and that disrupt the air flow. You want a smooth flow of air into the combustion chamber.
Smooth & unrestricted flow I agree, just wondering what would the ECU think? I've been considering removing those butterflies, but did you note any difference at low idle or low rpm?
Why don't you pull off the vacuum hose at the TVIS actuator and vacuum plug the hose. Drive around to see if you like it or not before you gut the TVIS. I believe your having the 225 engine?