JFTR, this was added in commit 72b59db126ebf39. Here's the comment in this commit:
Align partition sizes to sectors or user-requested alignment on all disk labels, unless on DOS and preserving some partitions (stay with cylinder-alignment in those cases). Currently I fear to change this code, since I'm not sure if the exception for dos disk labels and when preserving a partition is really needed or was just added com backward compability. Or should we just change it and give it a try? In which situtaions may we break things? Please help me to decide if we should change this. -- regards Thomas