Judging by how many people in the comments perceive YS as anti-communist propaganda and/or a revanchist Germanophile fantasy, overall quite a lot of people perceived this work incorrectly. Especially after Tanya fell into the same trap as Tatsuya Shiba, where people started praising what the author was trying to deconstruct or question.
But back to the topic, comparing the anime to the manga, I got the impression that the latter is primarily more vivid and emotional. For example, the manga has much more comedic or parodic elements, while the anime feels like Zen's straightforward statement on geopolitics and history. With an obvious satirical element, but still. If I understand you correctly, you want to say that LN itself, compared to both adaptations, feels like a much more serious commentary on its themes?
I haven't done any deep research, but reading the author's Twitter, I got the impression that while the audience largely perceives "lolis" and the animanga media as the root of the work, for Zen, the most important thing in YS is the messages he wanted to make.
