Understanding Atmel 9x60EK Shutdown Circuitry
By setting jumper J2/J3 the user can shut down the MPU without powering down its power rails


This is precisely the use case it's there for - you can put the processor in a low power shutdown state without powering down anything else that might need those supplies.

The POR pin on the MIC2800 is an open drain output and requires a pull up or pull down. When !SHDN, it will be pulled high through R17. Per the datasheet, POR will go low if either/both of the outputs goes out of regulation. Therefore, you can monitor the MIC2800_nRST signal to check the regulator output is healthy. When SHDN is set, obviously the supply will be out of regulation (as it's off), so it gets pulled low by Q5.