As a matter of fact, you don't necessarily have to be a developer nor a security enthusiast to have advanced knowledge about the system inner workings. Said this, I actually do support what you're saying (perhaps with another wording, but we get the idea).
The whole "if it's not broken why fix it" and "if you can pirate you are ok" is utterly bullshit. If downgrade check raises the concern about some titles being out of version/extra installed then is up to you to fix the issue. Maybe the system works fine, and maybe you can go all arrrr through the seven seas, but as long as we are human we all have different reasons to be in the scene. For me is not about the games, or the "free" content: it's about fiddling with the system. Under my point of view, having a clean sysnand is a must. I can't stress that enough.
Onto the thread's topic, downgrade check is right. You have four titles out of version and an extra title. Just for the downgrade results I'd say you have a new3ds (xl or not idk) and your downgrade went dandy fine. As another user said, you could check the "Random errors in n3ds" thread, but I'll advace that to you: you can properly downgrade the two first with sysupdater cia on sysnand and dowgrading to the same 9.2 package you used (n3ds!). You can downgrade the last two by grabbing them from the o3ds package as they are the same for both systems. And you can erase amiibo settings, as it is not needed. Be very careful when deleting titles as you could delete the wrong one (and then you'll be screwed!).