FT232RL VCCIO Configuration

I recommend you verify with FTDI datasheet as well as their support pages (they have a decent knowledge base). I have done a similar design:

You can use any of the CBUS pins of the FT232 to connect to the nBootmode pin of your chip. If the signal is the wrong way, then you can program the FT232 EEPROM to invert it. This means as FT232 powers up, it'll set those pins. You might want to employ a similar thing with nReset of your MCU, that way it'll remain in reset mode until FT232 is up and ready.

You'll likely need to manage separating the power bus using diodes such as a BAT54C or schottky diodes likes this:

Think about what would happen if both power ports are [accidentally] plugged in.

Regarding the PWREN#. It is meant for shutting down power of an external chip during USB suspend. It might be tricky in this case since it is low during USB enum, but it only goes high again during USB suspend which might prevent you from interacting with MCU. You might want use a generic CBUS IO and flick it up or down using the driver or one of the UART lines, etc.

Finally, most FT232 chips can't supply more than 50mA of current. Check that your MCU power requirement is lower.

Your original system was uncertain as the data sheet does not provide enough information. I'd guesstimate that it would probably work but this is not ceryain.

Your second method, with FTDI Vcc and VccIO both being operated from +5V has more chance of success. A possible issue is that the =%V line will now be one Schottky diode drop below Vbus but U4 is connected directly to D+ and D-. I do not know what level D+ and D- reach when at their maximum positive value but if they reach VBUS then the IC has SLIGHT voltage above Vcc applied to pins 15 & 16. I would expect that this would probably not cause problems as the IC is intended to operate "robustly" in an interface environment where "such things happen" but it may be worth keeping in mind if strange things happen subsequently. This may be covered in the data sheet - an exercise for the student :-).

Stop Press: I just checked data sheet - the two USB data interface lines are nominal 3.3V level signals so the above is a non issue. I'll leave it here as it covers something which can occur in this sort of situation so is instructional.