So, I also worked on this team (and am good friends with mjard). At some point there was a big decision made to heavily bias the engine against "unknown" executables. I said it was a bad idea then, and I still think it is now. The only way it can "know" about an executable is via its source, or its signature, or if it is on other users machines. This creates the obvious huge problem for "the little guy" distributing software. They actually think this is no big deal, and when it steps on toes, the distributor can just use their dispute system and eventually they will fix it. And if you don't like it, you can just get your software signed. I was of the opinion that this was bad behavior and unreasonable. They really liked what it did for review scores (surprise, we detect everything!). I lost.

Create a harmless helloworld.exe and put it on a random website. Download and run it. If things haven't changed since I left, it will get flagged as malware.

What I can say is that this has nothing to do with trying to crush the little guy or malice. With some exceptions, there is a general attitude there of not caring, or caring about the wrong things. Hanlon's Razor a little bit.