As far as I know, Calamares uses kpmcore as the back end for creating partitions during the installation. Kpmcore uses fdisk to do the partitioning. If you look at the man page for fdisk, the CHS referencing is deprecated and ever since version 2.17 of util-linux (package that contains fdisk), fdisk gets the sector size from the kernel and specifying the sector size manually is not recommended. This applies to auto and manual partitioning within Calamares.
It all boils down to you don’t have any control over the sector alignment within the installer. If you want total control of the sector size and alignment, you need to do your partitioning before running the installer and use something like fdisk, parted, gfdisk (or similar tools). Sectors alignment usually will begin at 512Kb, 1024Kb, 2048Kb, and 4096Kb. So if the first partition created begins at one of those positions, the sectors are aligned.
Thanks @eznix! If I understand well what you just said, I shouldn’t worry about sector alignment because that’s taken care of by the installation media regardless of whether you use manual or automatic partitioning. If I remember correctly, I used gparted from the installation media to resize the old partition and create the new one where EndeavourOS was installed.