Without a custom root option the "admix" dict source/dest values can contain non-monophyletic groups after rerooting, making it difficult to relocate the node index after rerooting (which you could otherwise easily find by using get_mrca_idx_from_tip_labels). The custom option allows you to reroot how you want upon reading the tree so that the admix dict values will be monophyletic under that rooting.
Without a custom root option the "admix" dict source/dest values can contain non-monophyletic groups after rerooting, making it difficult to relocate the node index after rerooting (which you could otherwise easily find by using
get_mrca_idx_from_tip_labels). The custom option allows you to reroot how you want upon reading the tree so that the admix dict values will be monophyletic under that rooting.