its correct toyota design but the atmosphere port is never left open, in original form it shares a port from the airfilter box or a port on the throttle housing depending on the version of 4EFE you have.
In simple words - any air that has to enter the engine will be filtered first.
how did your mechanic connect it btw - the original is a valve with a screw on top to adjust the rpm and is triggerd by the ISC pin on the ECU which sends a negative 12V to make it work.
Did your mechanic connect it to the ECU or just spliced into the compressor wiring?