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.