Plywood, properly installed over your planks, will be fine, regardless of where that joint occurs. NOw, if you were really paranoid, you could get thicker ply with a T&G joint, and make it stronger, but that is only needed when it is the first layer, since there would otherwise be nothing to keep the edge from deflecting. WHen you install ply as a second layer, those vulnerable edges are fully supported by the first layer. The only thing I'd look at is to potentially avoid having that joint exactly line up with what's beneath it, but since your first layer is on the diagonal and is T&G (?), it's not an issue either.
The idea of not hitting the joists with the second layer is to help decouple things some. Your planks and joists will want to change dimensions with the seasons (humidity changes), and the ply will be much more stable. With the planks and joists running in different directions, who knows which way things will try to warp to compensate...best to only have to deal with one. Using an uncoupling layer, like Ditra on top, can help with that seasonal movement much more than a rigid cbu board which primarily only offers tiling compatibility, and only a little decoupling.