Normally, a PCB will NOT have any firmware flashed onto the chips unless specifically requested by the designer, as well as only if the designer provided the firmware to PCBWay. An exception to this will be modules like ESP32/ESP8266 that are pre-flashed at the manufacturing factory (Espressif or AI-Thinker for example). It is also possible to ask PCBWay to flash a standard bootloader onto an Atmega chip, typically used in an Arduino-type device...
It is however quite difficult to give you a more detailed answer, as you failed to mention exactly what PCBs you are referring to.
I am thus limiting myself to giving you a generic answer, as well as trying to take into account as many possible scenarios as possible.