So, one of my questions I asked recently was suggested as being a duplicate by someone in the comments. I read through the question he said it was a duplicate of, and confirmed that it was different by adding a notice in the body of the question. A few days later, the question was voted to be a duplicate, despite me showing how it wasn't. What am I to do in this situation?
Honestly, it took me two looks to find the note in your question body where you disputed the claim of it being a duplicate. And you didn't really do that.
If you look at other questions that have been claimed as duplicate you can see that many put a notice about it at the top of their question, using different formatting to make it stand out and be easy to see.
Another point is that your current note basically boils down to saying: No no, this is not a duplicate., and that's it. If you really read the other question and then came to the decision that yours is definitely no duplicate, you will have found at least some objective points where your question differs. Put these points into your note, show the people why it's not a duplicate.
When people mark your question as a duplicate, they are saying that answers to the one could just as well appear on the other. Just saying that the two questions are different is not enough. Make them different. Acknowledge the things that you learned from the other question and emphasize what you want to learn from answers to your question.
I actually think that the practice of adding a message to a duplicate question is inappropriate. It's really something that would fit better in a comment than in the question.
The correct thing is to change the question itself. Read the other question. Look for what it does tell you. Acknowledge that. E.g. "In this [other question], I found that ... but that doesn't work for me because ...."
Both your edits are just arguing. They aren't telling us what you learned from the other question nor what you need from answers to your question.
Read the other question's answers
Part of the problem seems to be that the other question isn't giving the answer you want. You say that it doesn't apply, but what about:
The "Satellite Surveillance / ISS Live Feeds" section of this answer.
Or this answer, about an uninhabited island that no one visits because it is radioactive/poisonous/whatever. In your case, you don't even have to pretend that the island is uninhabited.
Or this answer about preventing boats from reaching the island and satellites from seeing it. Yes, it assumes that someone is actively making that happen, but is there a natural version? That would be a better question than your current question or the two similar questions.
In fact of the six answers, the only one that doesn't fit an uninhabited island is this one about making it look like pixelation. That really requires awareness of how satellite imagery works and active intervention. So five of six answers to the other question could appear on your question (one actually does, three times).
The answers suggest things like living underground, using electric cars, and other things to make the technology more low-key.
But as I demonstrated, they also suggest other things, that would fit an uninhabited island. I could see that at a glance the first time I looked. Why couldn't you?