So, I just need to add the correct configuration to my current hekate_ipl.ini file, and enter CFW on sysNAND just to use Daybreak and then I can just turn off and then boot again on sysNAND but without Atmosphere.
Now I see that the default ini file provided by sdsetup already contains that part, while the one I manually created following the "other" guide was missing that one (maybe one of the "issues" you mentioned earlier).
Since I am there, can you help me with this other line, first of all I am not sure of what it actually does (but now it worries me and I wonder if I should remove it).
bootprotect=0
(The easier way would be, I believe, to replace altogether that .ini file with the one inside the sdsetup zip file)
Painfully slow to go all the way from 2017 to 2023 with that tool... but managing to get there