This reads like Rudy Giuliani talking about the cyber.
The first time you booted into any firmware >= 4.0.0, without any NOGC patches, your gamecard slot was updated.
The method described in the first posting to get nogc patches up and working is defunct - at least as far as running atmosphere is concerned.
Atmosphere 0.8.1 should have automatically applied nogc patches to safe your ass - seems like you didn't use the most current version.
Other than that you could have doubled down and used these nogc patches as well:
https://gbatemp.net/threads/i-heard-that-you-guys-need-some-sweet-patches-for-atmosphere.521164/
Both of those methods work (even in combination) - and you should have gotten a "your gc slot doesnt respond, please reboot or contact nintendo" message on boot. If you didn't your gamecard slot firmware is updated. No way to downgrade.
What you "should do now" is up to you - "what is best firmware to have" is a silly game to play - that gets old after the first time (you are not the first one trying to play it though - so have solace in that).
You are getting the update nags, because you went online with your system. Having a ban deathwish or something. Asking for the yes please give me update nags, all the time Nintendo treatment. The intelligent persons approach would have been to use 90DNS (
https://gbatemp.net/threads/90dns-dns-server-for-blocking-all-nintendo-servers.516234/) even before installing a CFW - so Nintendo gets blacked out in everything you do online. (No online play either. No "easy" game updates. Thats the tradeoff, with Atmosphere - at least currently. (No emunand))
edit: Didn't step far enough into Rudy Guliani thought process mode.
5 Fuses burned means firmware 4.0.0-4.1.0 to begin with. So this guy didnt ever need to prevent the Gamecard slot update, because he always had it.
See:
https://switchbrew.org/wiki/Fuses
But hey - I also often start talking about stuff I have no Idea about what it means... Not.
Atmosphere 0.8.1 didnt apply the NOGC patch in his case - because he already had the update on the system (4.0.0+). Most likely.