The 3BAR (with tuning for it) will allow the ECM to adjust for and use boost levels above 14.7 psi, since the 2BAR MAP can't even detect them. These levels are primarily spikes and the stock Garret SHO turbos, per the manufacturer site, are only capable of maybe 17 psi or so max. In at least one dyno tuned SHO at LME more WHP was actually attained with less boost than the canned LME tune. Engines do differ, even in the same model.
My experience has been a much smoother performance overall, but especially in brisk acceleration, due to a more incremental sensing and transmission of boost data to the ECM... I confirmed this in a phone conversation with Dan Millen at LME after I added my 3BAR a year ago. I am much more pleased with my car since the 3BAR was added and have had no problems over about 13K miles. It is actually an F150 EB part... they have larger turbos on their 3.5TT GDI than the SHO. Will this affect your shift issue... dunno. Consider that any increased performance (tuning), if the power is actually used, increases stress/wear of the engine and drivetrain ultimately shortening lifespan. ...And like you I love "pole position" at a stoplight! So i have a bit of a leadoff too, LOL, and on the freeway I cruise at 80-90 mph with throttle response remaining very good.
Hope this helps... I would not be without a tune and I love the 3BAR overall performance. It is a relatively inexpensive, quick, and easy thing to try... If you don't like it, just revert.