I think you’re right about the extra chapters not necessarily being fixed points compared to main story chapters.I'd always understood
NTR as also encompassing the emotional side of feeling cheated/betrayed/stolen from even if in the cases where it doesn't physically happen, so just the perception/fantasizing of it happening would count, in that case.
If I'm incorrect, then disregard me on that.
I do see what you mean by gag comic first but also still containing story and plot/character progression, though. Part of my misconception probably has to do with the plethora of "extra" chapters that don't necessarily slot into the actual narrative, but do expand the character lore, as you stated, so not reading this super carefully/consistently makes it feel less cohesive than it actually is.
And I’m not an NTR enjoyer so I have a limited grasp on it. But I know there are multiple flavors. The version you describe
fits Suzu’s initial reaction to the thought of Yuu being “taken away” by Atori.
another flavor of NTR where the heroine (Suzu) is corrupted and stolen by the antagonist (Atori). But whether the NTR is really happening or not may just be a matter of perspective.