Yes. 'This' and 'so' both replace how late or shy she is being at this particular time and form a comparison She rarely arrives so/this late = She rarely arrives as late as how late she is at this time. She isn't always so/this = She isn't always as shy as how shy she is at this time.

They are almost the same. For a better understanding, it is helpful to compare three words: "this", "that", and "so". In many, but not all, situations they can be used interchangably. Situation #1: It is 10:00 and Emily has not yet arrived at the office. You can say to your co-worker: "Emily rarely arrives THIS or SO late". "That" is less suitable. Situation #2: Yesterday, Emily arrived at the office at 10:00. You can say to your co-worker: "Emily arrived at 10:00 yesterday. She rarely arrives THAT or SO late" (but "this" is less suitable). If you say she was late, without specifying how late she was, you can say: "Emily arrived late at the office yesterday. She rarely arrives SO late" (but "this" and "that" are less suitable because they have no clear referent. "So" is less dependent on having a clear referent.)

yes, this late / so late =very this shy / so shy = very