What if I wanted to put twelve thousand lines of code in a sample code block?
Will anyone ever have a need to do this though? You can just link it externally.
I take your point that markup doesn't need to count toward the character limit, and I agree the limit should be higher. But I also think there aren't many situations where it's absolutely essential for you to go over 12,000 chars, with or without formatting + links.
For what it's worth, I recall PM's position on this being "make your answer shorter then".