Well letters don’t really have a single canonical shape. There are many acceptable ways of rendering each. While two letters might usually look the same, it is very possible that some shape could be acceptable for one but not the other. So, it makes sense to distinguish between them in binary representation. That allows the interpreting software to determine if it cares about the difference or not.
Also, the Unicode code tables do mention which characters look (nearly) identical, so it’s definitely possible to make a program interpret something like a Greek question mark the same as a semicolon. I guess it’s just that no one has bothered, since it’s such a rare edge case.
Book burnings are bad when they are used to prevent the free sharing of information or ideas. It is a form of censorship. Burning the Quran is not censorship, because this is not an attempt to ban the Quran or prevent anyone from reading it. Its an entirely symbolic gesture. Its comparable to burning the American flag, which I’m guessing you’re not so against.