I’ve standardized on using a 5V FTDI board for all custom designs to keep it simple and avoid mistakes. When I need to reprogram a controller, the same FTDI board will work for any of my boards irrespective of being a 3V3 or 5V design.
On bootloaded designs I incorporate a FTDI connector. On 3V3 boards there is a voltage divider (3k3/1k8 to ground) for the mcu serial rx line. The mcu serial tx line is directly connected as is the reset signal from the FTDI breakout. Reset is ok as it is high voltage tolerant and the 3V3 from the mcu tx line back to FTDI is seen as logic high with no level shift required.
In terms of power, I have 5V on the FTDI power output as this can supply up to 500mA. This 5V is either used by the custom board or just ignored. On 3V3 designs it will be connected to the onboard regulator input and on 5V designs it is used directly as regulated output. On some boards I add a jumper that will allow me to connect 5V from FTDI or just leave it powered with whatever is normally used (you don't want to connect two independent supplies to the same rail).
This way I can program all bootloaded boards with a single FDTI without worrying about level conversion and having the flexibility to supply power if needed/desired.