*update*

May be it doesn't have to be done at the tree creation level. It could be
using loops and creating two different balltrees. Something like

tree1=BallTree(X,metric='metric1') #for x-z plane
tree2=BallTree(X,metric='metric2') #for y-z plane

And then calculate correlation functions in a loop to get tpcf(X,r1,r2)
 using tree1.two_point_correlation(X,r1) and
tree2.two_point_correlation(X,r2)
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