I am wondering why, with Goldleaf, some nsp files require me to have loaded Atmosphere via Hekate->Launch CFW (emuMCC) and others require me to have loaded via Hekate->payloads->fusee-primary?

That is because there are 2 sets of patches; one for Hekate/fss0 and one for fusee_primary. However there isn't any scenario where games would only install with one set of patches especially if you have both which seems to be your case. Its more likely that Goldleaf is the problem here as it is arguably the worst title installer. I recommend switching to TinWoo Installer instead.I am wondering why, with Goldleaf, some nsp files require me to have loaded Atmosphere via Hekate->Launch CFW (emuMCC) and others require me to have loaded via Hekate->payloads->fusee-primary?