One would think that, but it is nearly impossible to seal a butterfly valve without some sort of gasket material on the ends. Try it with the throttle body (block off the IAC and bleed screw if applicable) the TB leaks too. Some leak more than others but every one I have is like that (more than 6). I toyed with the idea of adding an o-ring but it ends up tearing. Having an insert that is made of a softer material would do much better for sealing but it will wear out eventually (that’s why industrial valves are rebuildable).
You can cap the bypass off if you like and it should increase boost some. There is also a hose that runs from the lower IC tube adapter to the SC inlet plenum. This is known as the crosstalk tube, and it’s there for a reason. Do a search for crosstalk tube.
Jeff