Hi byeongjinkim,
I checked the toolbox initialization and configurations. There are no particular settings involving the Voltage Regulator Control Register (CPMUVREGCTL) therefore this register will have the default values after reset.
According with the Reference Manual both EXTXON an INTXON have reset value 1's - which is confusing.
I agree with you that we need an initialization sequence according with this table in order to specify the exact setup.

Same story with BCTL and BCTLC pins. No initialization done from Simulink Toolbox.
In order to address this and configure the target the way you want, i think you can use the PEX to generate the configuration headers and then you can inject that code via S-Function into the Simulink generated code. That would do the trick in this case.
Hope it helps!
Daniel