Oh right, yes, good point! Thanks for your patience on this.
Rewrite-clj digs deeper into tools.reader than most users might.
It makes use of clojure.tools.reader.reader-types namespace using fns like read-char, unread and peekchar. It takes this lower level approach to return things the higher level reader fns do not return, like whitespace, comments and #_ :skipped-stuff.
So when rewrite-clj gets that whitespace, the newlines are always \n (even if they were originally \r\n).