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 3V3 designs it will be connected to the onboard regulator input
you don't want to connect two independent supplies to the same rail)
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