Could not find that part of the letter—mind quoting the passage supporting this claim?
If they were really for free speech, period, that's what they would say. But they don't say that. They say they are for "the free and unfettered conduct of scientific research and debate". But who gets to decide what counts as "scientific research and debate" and what doesn't? They do.
Also: who says they do decide what’s scientific research and debate?
Because that is how academia works. And they're all academics.
No, they're not. Scientific research and debate are not the only topics that get discussed at academic institutions; in fact no topic should be off limits for discussion at academic institutions. Nor should the institutions themselves have any privileged position in deciding what counts as relevant for a particular topic, whether it's scientific research and debate or anything else.
Do you think that these same scientists would claim that researching, say, eugenics, is an acceptable use of an academic institution's resources and brand name? If not, who's drawing the line and what is the line?