Other Parts Discussed in Thread: TPS53355
With PGOOD pulled up externally to an MCU or FPGA and an external voltage source, I would not expect any issues in the soft-start/mode selection so long as the probe monitoring PGOOD is relatively high impedance and PGOOD has a reasonable pull-up resistance to its logic voltage. As the part starts up, the PGOOD pin will assert low and the device will output a current on the MODE pin. The resulting voltage is read to set the soft-start time since the pin voltage is referenced to ground at this point given the PGOOD FET is on. The part will start up and then begin switching in FCCM once PGOOD asserts high (in which case the FET driving the PGOOD logic turns off) and in the case where the MODE pin is connected to PGOOD with an appropriate resistor identified in table 7-3.
I understand the potential confusion as the RF pin is referenced to VREG when the device registers some of its available switching frequency settings. Please be assured that the MODE pin is referenced to PGOOD or GND depending on the choice of FCCM or auto-skip respectively, and I do not see any issues with the setup in which MODE is connected to PGOOD and there is high impedance I/O pin monitors PGOOD on the TPS53355/53 devices.