The VE will be affected by everything between the throttlebody and the exhaust housing but not much more than that. So, intercooler, compressor housing, charge pipes, exhaust, all of that should be irrelevant as far as the VE is concerned. What those things might affect is the pressure and temperature of the charge air at a given condition (i.e. idle, boost, etc) but the SD code will account for pressure and temp when it calculates flow so it should not require a retune. Of course, that assumes perfect sensor response. In reality we see a significant time delay on temp sensors so the intercooler in particular will affect the tune to a certain degree.