The reason there are detainees and enemy combatants in addition to POWs is that a POW is someone who was fighting under the banner of another state. If the person isn't wearing a uniform or if they fight for a group that isn't recognized as a state, they are not generally a POW. "Rules of war" apply to POWs in this system.

Boy that sure would be messy if we ever ended up waging war on a series of nebulous non state actors.

Exactly the point!

There's no contradiction of principle, a US citizen can fight against the US in a war without the US having declared war on that individual.

It's happened, some number of US citizens fought for Germany and Japan in World War 2 (and paranoia about it lead to the Japanese internment camps).

One driver for American internment camps for Japanese citizens appears to have been the actions of several Americans of Japanese descent immediately after Pearl Harbor - the Niihau incident: https://en.wikipedia.org/wiki/Niihau_incident