The boost pressure on a simple turbocharged car (and on your 2.0LPT until you upgraded it) is governed purely mechanically by the wastegate actuator. This consists of a diaphragm with one side connected to the manifold so it has boost pressure acting on it and the other side at atmospheric pressure. Under boost, the diaphragm moves the wastegate in the turbo, which opens and lets exhaust gas bypass the turbine, limiting the amount of energy available to turn the turbine, thus reducing the boost pressure. This is designed to reach an equilibrium point at a desired boost pressure, thus limiting boost to that pressure.
On the Saab engines, this particular pressure is called "basic boost pressure" or "base boost" for short.
On engines with APC (like yours has since it was upgraded), there is an electrically-operated valve (the APC or BPC valve - different names for the slightly different designs used over the years, but essentially the same thing). The ECU can use this to bleed pressure away from the wastegate actuator. This means the actuator "sees" less pressure and doesn't open the wastegate so far. It now takes more pressure to open the wastegate (because only some reaches the wastegate actuator) so the effect is an increase in boost pressure.
APC can increase boost pressure beyond base boost, but can't reduce it below that level. If there is enough exhaust gas flow to achieve base boost, you'll always get at least base boost pressure.
Now, what I found when fitting the JT exhaust (and a few others, but not everyone, have also found is that the base boost pressure drops a bit after fitting the new exhaust. I'm not 100% sure of the theory why, but that's what happened on my Aero. On Trionic cars liek yours, this will have no effect on maximum boost pressure, but it will affect how it behaves at lower boost pressures. In particular, my Aero felt a bit gutless in the mid-range - the turbo lag was increased.
It's worth checking your base boost with a cheap boost gauge, especially since your car probably doesn't have a boost gauge built in.