VRC4173..( uPD31173 ; companion chip for VR4100 )

When not using the USBU of the VR4122 companion chip (VRC4173), is 48MHz clock input necessary?
Also, regarding the 48MHz clock input pin handling, can the pin level be fixed to any level?

No, 48MHz is not required when not using the USBU.
Clock input pin handling is unnecessary, but a software measure is required.
Stop oscillation and mask the48 MHz clock.

Concretely, set MSK48MOSC, MSK48MPIN, and MSK48MUSB to 0 in the CMUCLKMSK (base + 0x40) register.
Also, the 48MHz clock is the FIR base clock of the VR4122.
When using FIR, oscillation/supply is required.

Of the PCI signals connected to the VR4131, external pull-up is recommended for FRAME#, etc.
If the power supply of the VRC4173 is controlled by the MPOWER signal of the VR4131, I think that the power supply of the VRC4173 goes ON after the power supply of the VR4131 goes ON.

In this case, should the pull-up connection be made with VDD3 of the VR4131 or VDD3 of the VRC4173 ?

Pull up the PCI bus by the power supply of the VRC4173.
When the power supply of the VRC4173 is controlled by the MPOWER signal, the power supply of the VRC4173 is switched OFF when the VR4131 is in the Hibernate mode.
Since the 3.3V system of the VR4131 is always ON, the absolute maximum rating of the VRC4173 is exceeded in the Hibernate mode.