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@azrobbo
I can answer your question regarding the meaning of the 3.3v label on the reference diagram.
The pins labeled "3.3v" are only tolerant of 3.3v input voltage. Whereas, the pins without the "3.3v" label are tolerant of up to 5v input voltage. The data sheet has a pinout table on p 30-35, where this can be verified.
I do not believe the output voltage is any different on those pins, but I'll defer that to Gordon.