The galvanic isolation in the CAN interface shall protect the CAN controller and also the PC from high voltage incidents on the bus. Under certain circumstances, the voltage differences in a CAN network can reach values far beyond specification. This can not only destroy CAN transceiver and CAN controller in the interface, it might as well have an impact on the PC hardware. In case of overvoltage on a PC card, this might be forwarded via e.g. PCI or PCIe and the motherboard can be destroyed as well. In seldom cases we also experienced USB host controllers were destroyed by such effects.
With an isolated can bus, you still might have a defect on your CAN interface (in most cases the CAN transceiver), but your much more expensive host system will not be affected.
Galvanic isolation is not between bus and CAN transceiver but between CAN transceiver and CAN controller. Reason is, that the CAN transceiver is the amplifying component which provides the voltage levels for the CAN bus (similar to MAX232 on serial RS232 communication).
CAN transceivers have a certain tolerance which is rather high considering the voltage levels defined for CAN. According to ISO 11898-2: -3 V to +16 V ( up to +32 V for vehicles with 24 V voltage supply). CAN transceiver datasheets often state up to 36 V.
If there is any voltage difference on the bus which exceeds this tolerance, the CAN transceiver might be destroyed or corrupted.
CAN-GND is not used as a common reference voltage level for the CAN signals
EMI issues such as induction by drives, inverters or other machines using high voltage or high frequencies