If you use the common B9S + Luma combo as described in many guides, B9S is in a kernel partition and Luma is in the root of the SD or ctrnand, named "boot.firm"
In this case the bootrom only loads, verifies, and runs B9S - what happens next (the two fixed possible sources, the mounting of sd/ctrnand, etc) are 100% up to B9S
B9S can be substituted with other compatible bootloaders like fastboot3ds or godmode9, which may or may not implement things differently (spoiler: they do), for example giving you more or less choice of sources of kernels to boot and extra options
There's no technical reason for which Luma cannot be installed directly as the kernel to boot; the developers simply chose to not support being booted that way (for reasons related to discontinuing CakeHax/A9LH versions - they weren't interested in supporting different initial environments and the different potential issues that come with that)
B9S by itself doesn't even offer "the ability to boot multiple different payloads" unless you really want to stretch the SD-first-then-try-ctrnand design