Is there a reason why Kosmos uses fusee_secondary?
Wouldn't it be easier to provide the same patches as the ones for fusee_primary and a hekate_ipl.ini to launch atmosphere with fusee_primary? Or to convince Kosmos devs to do that change in the hekate_ipl.ini they provide.
That way there would only be one set of patches for every configuration.
The reason why they do it, is because it is the only way to have sysnand and emummc entries on boot. Chainloading fusee primary will always boot emummc, unless the emummc.ini is changed. Via fusee secondary, they can choose whether sysnand or emummc should be booted, and then give you some nice booting options when running Hekate. But still, not much a need for that: they could just provide a emummc entry (via fusee primary) and a "stock" entry (via fusee secondary, which does not require any patches for stock) and let people boot emummc and stock sysnand.
The only catch is that there would be no way to boot
sysnand with CFW
and use fusee patches, as disabling emummc on boot requires fusee secondary, as I explained. This can be solved by using some homebrew that let's you flip the config in emummc.ini, reboot to hekate and choose the emummc entry (which chainloads fusee primary, and then will load sysnand CFW this time).
That is why I still believe booting directly with fusee primary, bypassing Hekate completely, and using a emummc swapper homebrew is the simplest solution. No burned fuses, no messing up with fusee secondary, and boot whatever you want. The catch here is that with fusee primary you can only either boot in cfw sysnand or cfw emummc. Booting stock sysnand requires shutting down the Switch and booting it normally (with Nintendo's official bootloader), which burns fuses which (i still need to understand why) seems to be a concern for many.
Even CTCaer, the author of Hekate, just burns fuses without worrying.
However, booting sysnand with cfw (at least on my side) does not lead to any ban, as long as you don't do anything illegal, and just use your switch normally. Been doing it for two years now, and still buying games from the eshop. So, one can use sysnand with CFW as their "stock" sysnand for non homebrew related stuff.
Of course, if you go
online (even with emummc)
and download games illegally with hbg shop, your emummc (and thus your sysnand since one is a copy of the other) will likely be banned. You might use incognito or Dns, but it is not clear whether they really help.
So, my suggestion is just use the fusee primary payload with your RCM payload sender, boot whatever the emummc.ini dictates and just flip the config with homebrew if you want to move from emummc to (CFW) sysnand, and vice versa.
However, if booting stock sysnand without burning fuses is important for you, then use Hekate, and just change the hekate_ipl.ini as I suggested above (this is also explained in
this tutorial). In both cases, you can then use the fusee primary patches, when on emummc.