I’ll take a stab at this and allow others with more detailed knowledge correct any mistakes I make and fill in any gaps.
Hekate is a bootloader. I think of it like a BIOS. There is a normal “BIOS“ already inside the Switch that gets all the components (like usb, sd card, screen, digitizer, etc) powered up and communicating before it hands them off the OS (and does things like checking for burnt fuses.) The stock system is hard coded to boot nothing but the Horizon Operating System (HOS). Hekate is ”injected” to interrupt the normal ”BIOS” process and allows us to skip and alter some of them and ultimately hand odd to our own stack.
Original Firmware (OFW) is HOS.
Custom Firmware (CFW) is Atmosphere. Atmosphere isn’t a replacement OS but more like a custom set or wrappers around the original HOS that makes it behave the way we want and break out of the walled garden. SXOS and ReiNX were similar alternate CFWs that, again, were not replacements of HOS.
L4T and Android are examples of Operating Systems that completely replace HOS.
One of the advantages of breaking out of the system is we can ignore or modify things. Things that would require code to be cryptographically signed in order for HOS to run it no longer have to be under CFW. This enables homebrew.
Homebrew apps are unsigned programs that interface with the OS and make it so things it originally was not intended to do. Since the entirety of the Os has been laid bare we can pretty much do anything we want within the limits of the OS and the hardware. Sky is the limit (as long as the OS and memory, CPU, graphics etc etc will allow it.)
I’m going to stop there as I’m probably already stretching things beyond my knowledge and making some real OGs cringe with my noobness.
So to answer your question, by using Hekate as an ”injected” BIOS to boot the stock OS…
Hekate hands off to 100% OFW and HOS then runs as if you have not modded the console.
I'll try to rephrase by my own words just to be sure I understood your words.
Ok, so from what I could understand, the stock bootloader still runs some code until Hekate comes in and stop it so that we can have some control over the initial processes. Am I, at least, close?
Then, when we choose to launch Atmosphere, it will also stop HOS from running alone, allowing us to do things we wouldn't be able with HOS unless those changes could be cryptographically signed so that they could be "seen" as legit by HOS.
Am I close here to?
But in the end, this was not my initial question. heheh. But it was also a question I wanted to know more about in a near future.
As of now, my main interest was to understand the custom and otiginal bootloaders, custom and original firmwares, custom and original OS'es so that I can keep track of what people say and understand what they say.
As an example, I was confused when you mentioned "stock bootloader" because I don't even know if there is a specific name like we have for Hekate (which I take as a custom bootloader).
And when we call firmware to Atmosphere, I mean, firmware can be any piece of code we load onto a chip, as far as I'm concerned! Operating system is also a firmware but at a higher level, which allow us to interface lower layers (hardware, protocols, etc) with higher level laayers such has software running on top of an Operating system! So, this is confusing to me!
For instance, something like this table, would be clear to me:
ONB - Original Nintendo Bootloader
ONF - Original Nintendo Firmware (the files we download with versions like 14.1.1)
But I think things cannot be separate just like this.