Sounds like a good idea to me. We also are transitioning to milpa growing as our go-to after growing three sisters for the first time last season.
I think the answer to the first question is yes until proven otherwise. We have a lot of mature black walnut on our place and I feel like I may have seen things growing fairly close that are on the juglone-sensitive list.
An answer to the second question is more involved, but there is probably nothing easy about it. It might be relatively easy for a plant to gain advantage over its peers by being slightly more juglone tolerant. But with no steward guiding the selection of this trait and a huge non-juglone containing ecosystem in which to live and reproduce, it’s unlikely this trait would cause such dramatically better reproductive success as to become firmly established. And in the unlikely event that it did, there’s still all the other juglone-sensitive plants. And if somehow such a large subset plants naturally become juglone-tolerant that it began to encroach on black walnuts, now black walnuts that produce more juglone, or juglone together with another allelopathic chemical, might enjoy greater reproductive success than their peers.
So while I’m confident allelopathic resistance is breedable, I doubt it would be possible for it to arise naturally, firmly, and generally in the wild to the extent that the strategy of producing allelopathic chemicals is rendered ineffective.
I think @Joseph_Lofthouse has had good luck intercropping pole beans with sunflowers.. We might buy trying sunflowers in a milpa this year and can let you know how it goes for us 
let us know how you go!