Sometimes you start with the clear case, then extend the conclusions to murkier cases. That citizens have certain enumerated rights makes violations of those rights easier to debate to a meaningful conclusion. It's not that "nobody else counts", it's that if citizens don't have those rights protected, others surely won't.

In the case of the "late unpleasantness", "war of Northern aggression", "war of secession", "civil war", whatever you label it: those targeted had declared themselves a separate country, wore uniforms thereof, and operated in clear cooperation for military ends. Be that deemed international war, insurrection, etc it was clearly under conditions where individual trials were infeasible, akin (at minimum) to police attempting to take down an armed gang violently resisting arrest: trials only work when the defendant is engages in docile participation in the judicial process.

And yes, if one is not operating under insignia (usually of a nation) in war, to wit a citizen acting treasonously out of uniform and out of organized conflict, largely independently, there is indeed the option of "trial in abstentia" and sending in special forces to extradite - with extreme prejudice if necessary.