Yeah, the comparison logic is pretty simple right now (see my comment). Unfortunately, `\not\in` and `\notin` look slightly different.
We're figuring out the best way to accept slight variations. It's a tough problem and isn't as simple as increasing the pixel threshold. For example, replacing a + with a - has an extremely small pixel difference (and the two characters have the same width, so it doesn't affect anything else), but we shouldn't accept both.
You shouldn't accept slight variations IMO. One of the primary motivations for TeX (also the largest chapter in The TeXbook) is "Fine Points of Mathematics Typing". If someone types something that results in slightly different output, that is a good teaching opportunity (maybe highlight the visual diff in red or something) rather than simply accepting it.
We're figuring out the best way to accept slight variations. It's a tough problem and isn't as simple as increasing the pixel threshold. For example, replacing a + with a - has an extremely small pixel difference (and the two characters have the same width, so it doesn't affect anything else), but we shouldn't accept both.