What is the significance of this if any? I also wanted to remove that logo after not having it for a while and then suddenly having it after updating.
There are two ways to load Atmosphère FROM Hekate:
On mode FSS0 where Hekate act as a full bootloader then read and extract some parts from Atmosphère PACKAGE3 file and load them.
On Payload chain mode, where you chainload FUSEE.bin file from Hekate, on this mode is Atmosphère who make all the bootload process.
If you modify the source files and build your own Atmosphère, you will need to repeat the process on EACH update.
If the only splash you want to ride of is "Splash.bin" you can opt to use Hekate for loading Atmosphère as FSS0.
you also can load Atmosphère injecting or loading FUSEE.bin from start and not using Hekate at all, on this case the only way to ride off any splash is to build your custom Atmosphère from source.