OK - paragraphing often is a matter of opinion. fwiw, it drives me crazy when I've read papers by friends doing phds & I think their writing is appalling. I don't care what subject they are writing about - they should be able to communicate their findings.
forget about any examples from fiction - that is a completely different.
If you're writing in a formal situation (e.g. essay) then you should follow the rules. The example of the 3 sentence paragraph is for a main paragraph asserting a particular point. I teach students to make sure that they PEE in every paragraph (point, evidence, explain). The explanation is often the key part and should be at least one sentence long. The PEE components don't have to go in a particular order, and I think that could lead to what you're trying to do.
Linking paragraphs, that form a bridge between one point and another can be less than 3 sentences, but they smooth the transition. I would always try to make them 2 sentences anyway, just to keep the pedants happy.
If you're putting a sentence by itself to make it stand out, then that's a problem. It's a style used in fiction to get a reaction from the audience. In an academic paper you shouldn't be giving highlights, or getting a response, it is supposed to be as objective as possible. I suspect that what you're doing is rounding off a point with your opinion/findings/reiterating the point or something like this. Then that sentence should be in a paragraph with the material it is relating to. (Don't put a main point by itself)
That bit in brackets is what I suspect you are putting by itself. It's the finale of the paragraph, not its own point, so shouldn't be left out in the cold like this. Keep it with the paragraph that it belongs to.
When someone is reading your work, they will subconsciously pause whenever you start a new paragraph. If they then realise that the thought should have been part of the previous paragraph, it disrupts their flow and can be annoying as it give s a 'disconnected' feel to the ideas.
It can upset a pedant.
Anyway, before this turns into an essay of its own, one last point.
Whoever is grading the paper is right.