Well.... The wastegate actuator is trying to regulate the amount of pressure increase the turbo compressor is providing. It does this by moving the exhaust gas bypass valve, aka wastegate puck. Spring holds it closed, pressure opens it.
This is a simplified explanation. Not going to go into the effect of exhaust forces on the wastegate valve etc. The theory can get pretty deep.
The movement of the actuator is the result of balancing the force of air pressures versus spring force. When the air pressure difference on the diaphragm gets stronger than the spring force, the spring compresses. The actuator moves, opens the bypass, and the turbine slows down. The boost is lower, and therefore the air pressure holds at this level, with the actuator partially extended.
A normal 'blow through' system (majority of turbos in the world today) has an actuator which is sensing turbo compressor OUTLET pressure by a hose connection to the turbo, and balancing it against the spring. The other side of the diaphragm is open to atmosphere. The turbo inlet is also open to atmosphere without restriction, so the pressure is the same on the turbo compressor inlet and the wastegate actuator 'rod end.' Therefore when the turbo is raising the air pressure at atmospheric pressure, to the boost setting, the actuator will feel the same pressure as the turbo compressor.
With a drawthrough system, you introduce a new effect. You have a throttle body on the turbo compressor inlet. When the throttle is at less than WOT, the turbo compressor is receiving less than atmospheric pressure. If the turbo wastegate actuator does not have the second port connected to the turbo inlet, the wastegate will try to maintain the same turbo outlet pressure (relative to atmospheric pressure) as the throttle is closing. This causes the turbo compressor to speed up, making a high vacuum below the throttle plate. As the boost is reduced by closing the throttle, the wastegate is going to try to regulate the boost UP, by speeding up the turbocharger. Because the compressor is becoming 'unloaded' by losing air density on the inlet side, it will pose less of a load on the turbine, therefore allowing it to speed up. This will put more restriction on the exhaust, more heat on the turbo, and more centrifugal forces on the turbo components.
With the drawthrough system connected as designed, the wastegate actuator is working just like the blowthrough system. The compressor OUTLET pressure is acting on one side of the diaphragm, and compressor INLET pressure is acting on the other. The only difference is, here a hose connection is required at each end. One hose from the compressor outlet to the actuator base end; another hose from the compressor inlet to the actuator rod end. This configuration ensures pressure is the same on the turbo compressor inlet and the wastegate actuator rod end, as well as the compressor outlet and the actuator base end. When the throttle is closing, and the pressure at the turbo inlet is falling, the actuator will have less pressure on the 'rod end' and therefore it will take less pressure on the base end, to extend the rod. The pressure across the actuator diaphragm is the same, so the turbo compressor pressure rise is the same.