- Edited
Not clear which ISO you are using, but any of the latest ISOs have BTRFS as option in the erase drop-down (not replace, that is newly added in upstream Calamares, but not tested much, so not included here, simply editing /usr/share/calamares/settings.conf and adding it there is not enough to make that feature work).
But in all, might be a good idea to understand what KaOS is and what it is not before installing, especially the part about limited repositories:
https://kaosx.us/
https://kaosx.us/#goals
https://kaosx.us/#repo
https://kaosx.us/about/
As for bootloader, systemd-boot is default here (you can select no bootloader or rEfind), makes no difference how the bootloader part is done whether you use automated or manual. In your case, if you have many installs over many partitions, it is better to use rEfind (or no bootloader, and let the bootloader from another install add KaOS).