Yes, factory supplied devices have the bootloader installed.
EA is held high for internal program space,
PSEN is brought low,
RESET brought high, then released,
PSEN released to a high state.
This will cause the bootloader to execute in a 64/52 pin device.
In the 32 pin device, the BLJB bit determines which program space is pointed to. From the factory this bit is set to point to USB bootloader, but once you change it, you loose it. In this case you must use a parallel programmer to change the BLJB bit.
The bootloader can be overwritten as well. In this case you must parallel program the code back. Code is available from the Atmel website
Your 89C5131 data sheet gives you all this info.