That is distinctly odd! I cannot think of why they would do that, except for those who are applying to more than one specialty. I think I used the US grad form last year so I can't tell you if it was there on the IMG form.
As you say, the whole point of a LOR from a pathologist is that it is specialty-specific.
It's nice that your third letter-writer called to confirm the point. I would tend to agree with her, it would be a lot more convincing to write about your interest in Path especially if they know you well.
I can understand your concern - there is the small risk of "not following instructions", so to speak, but I highly doubt that the people who scan LORs for ERAS would bother reading through each and every one of the letters to make sure they weren't targeted towards a particular specialty. They have more pressing matters to deal with when the season is in swing.
Your personal statement is going to be all "GO PATH!!" anyway.
Maybe you could pretend you "didn't see"? 😉
