Just popping in to say that I'll continue to independently maintain SDSetup, PegaScape, and probably switch.homebrew.guide (this ones a little tougher since we need a place for user support, working on that).
Everything will be adjusted to remove AtlasNX and Kosmos specific stuff. SDSetup will...
The "Archive Bit * AutoRCM" is just a tab with more menu options. Hekate will never let you enable AutoRCM on an IPATCHED Switch, so there is no worry of enabling it (from Hekate, YMMV in other homebrew). I'll update the guide to mention this.
Sleep causing problems sounds like Hekate might be...
The total time taken is because you are chainloading fusee-primary which takes eons to load. Try just loading CFW with only Hekate. You can specify fusee-secondary as an fss0 in a hekate ini and it skips all of the fusee waiting nonsense.
Hekate itself had plenty of issues alongside Atmosphere (both each had their own issues booting certain firmwares).
They are currently being posted on the RetroNX discord. That's the only place to follow updates until a proper release is posted on GitHub.
There is a pre-release build on RetroNX which fixes booting on plenty of firmwares and a bunch of emummc fixes. The build J is packing is the r3 version of that build.
This only deletes the update files from your system. It does not reset the update record nor vulnerability!needs_update_vulnerability_policy flag in ns which you are guaranteed to get at this point. These flags force you to update to access the browser webapplet.
If you ever want to add CFW packages to the application in the future (SwitchBru's options are pretty limited iirc and don't include sysmodules), feel free to use SDSetup's API. See here and here.