I'd go with the 650c wheels
I had a bike once with 700c wheels and a sloped top tube. This meant there was less room at the headset to adjust stem height - actually in this case there was NO room to adjust the headset as it was already higher than the seat and could not be lowered. I rather doubt Sweetpea's design using 700c wheels would be anywhere near that bad, but as has been pointed out and as I think you acknowledged, there have to be trade offs in smaller bikes with 700c wheels.
Your adjustment options will be much better with the 650c frame, but since this is a custom fit I rather doubt you'll need to adjust much. Still, you never know how things might change for you. You'll have more leeway with the 650c.
Yeah, tires may be an issue. I've got a 24" front wheel so I know a little bit about that. I just carry a spare innertube for each tire and a spare 24" tire on multi-day or non-SAGged long rides. On a SAGged ride, I don't see why a SAG vehicle wouldn't be willing to carry the spare for you if you asked.
Some people may tolerate a particular trade-off (or two) better than others; I'm 5'2", but I'm so short-waisted even for my height that I cannot deal with the tradeoffs that have to be made to make a 700c bike "fit" me (actually can't be made to fit me). It's not just about height, but about the whole package and your particular body characteristics.




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