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Looking at the code, it seems to me that the functions implementing local and global heights are wrong. The global height of an individual algebraic number is, I think, correct (and I seem to remember that I wrote it) but the height of a point is projective space is certainly not the max of the heights of the coordinates -- for a start that is not well-defined, as already remarked. I'll make a sage trac ticket for this, and may even fix it myself.