nazca #252735 Keep distance matrix by default [validation pending]

Currently, we do not keep the distance matrix in get_aligned_pairs, and thus, we do not correctly threshold on the distance.

prioritynormal
typebug
done in0.6.0
load0.100
load left0.000
closed by#1615cd653f1d [aligner] Keep the distance matrix by default, closes #252735
patch[aligner] Keep the distance matrix by default, closes #252735 [applied]