I'm guessing The Startup is looking for a different article format. I've skimmed through 10 articles listed on their front page and it looks like 9 of them are listicles, e.g. "7 Steps to Creative Mastery...", "4 Ways to Optimize Your Article Output...". It would take quite a stretch of the imagination to convert your article into a listicle, which I suspect might have made it less likely for them to accept it.

I also noticed that all of the articles have very short paragraphs. 3 sentences per paragraph. Sean Kernan veered once into a 6-sentence paragraph, but none of them are 16-sentence paragraphs like what you wrote in point 4 (towards the end of your article).

I guess The Startup is swamped with submissions and, as such, aren't willing to veer away from a formula they're comfortable with.

It is a shame though, because I agree with a lot with what you had to say.