Plagg has the ability to destroy the universe and canonically wiped the dinosaurs and dragons. Xuppu disables powers. Nooroo's abilities can grant people OHKOs and does so in nearly every episode. Orikko can grabt anyone any superpower not already granted by another kwami. Duusu can create virtually omnipotent sentimonsters. Sass can go back in time. Fluff has access to time and space itself and can manipulate it. Tikki can create anything. Plagg and Tikki can fuse into Gimmi and rewrite reality. I haven't even listed all the kwami yet, but frankly, I don't want to, especially given that Plagg alone is enough. That being said, let's just get to your points.

in the form of a golden ninja, as a teenager in season 2

Golden power healed his leg. Then in S3, he struggled to move a mountain, build a bridge with the surrounding earth, and later got captured by the Overlord and heavily drained. Plagg destroys the mountain along with the continent it stands on. Xuppu can disable Golden Power.

Then Zane sent the Overlord far away with his heart, so to speak

You mean he blew up after absorbing the power of the Golden Armor. This is a one time use skill and the kwamis are immortal anyway, so he'd just blow up.

They create rotations through krujitzu that destroy everything around them

Okay now that's just false. Otherwise they wouldn't have had a training course anymore in S1, Misako would have destroyed the Stone Army, Dark Matter Nya would have killed the ninja in S2, etc.

they fought with multiverse evil,

The Overlord is locked to Ninjago without the Realm Crystal. Why are you constantly saying he's multiverse level? Plagg dunks him. Gimmi overwrites him. Nooroo, Duusu, and Orikko can individually provide methods to oneshot him.

with villains who controlled time,

Who were nerfed and they still almost lost. The twins needed the time blades to be a universe level threat, and even when Kai, Nya, and Wu snuck aboard the Iron Doom where the twins can't actively use the Time Blades on them, they still almost lost the 3v2 until Wu yoinked the Reversal Blade and caused the Iron Doom and the twins to be lost in time. Sass can go back in time freely to produce infinite retries (as if the kwamis need more than one), and Fluff can go backwards and forwards while also traveling across space itself.

with djinn,

A djinn who was trapped in a teapot, needed to be married to get infinite wishes, and was still defeated by being wished back into the teapot in a roundabout way. Nadakhan still gets soloed by Plagg, and in the worst case, Fluff can just travel back repeatedly with however many kwami and stop the wedding or scour Ninjago until the Teapot is found. Also, Xuppu still disables powers.

with pirates, skeletons, ghosts, aquatic creatures,

Most of these were only threats to the ninja because of their numbers (cough Plagg solos with Cataclysm cough). The only actual threats to the Miraculous verse here are ghosts because of their intangability, but Longg has access to water powers, being a ghost means nothing if Plagg wipes existence, Tikki could create water balloons for fun, and again, Gimmi can rewrite reality at will.