According to the available schematics, the switch is configured (via bootstrap pins) to come up in "CPU mode", i.e. all ports come up with disabled links until the switch is configured by the CPU.
Actually your assumption in your figure 3 is incorrect, all current switch ICs I know allow bootstrapping to come up in isolated mode on power on. Save any errors by the HW design engineer, it is completely fine to use a switch for isolation.
The 2.5Gbps link speed allows to stream 1Gbps to each LAN port concurrently (e.g. some data coming from the SATA port, or the USB 3.0 port, or something else connected to the mPCIe port, e.g. PCIe-to-SATA).
