Oh gosh, there is a lot of thinking here about something we usually say without thinking!
J:Are you free now?
T:No, I'm *so busy. (very)
J:Why are you always so busy?
Yes, I think there is surprise at the extent of T's busy-ness. "Why are you always busy?" shows some surprise too, and that is why J is asking the question. But "Why ... so busy?" implies surprise at the extent
, eg: 'so busy (that you can't help me)' or 'so busy (that you can't go out for lunch.)' So yes, the extent is unexpected, so J is surprised.
(By the way, it seems to me that "Why are you always very busy?" is not a question that would be asked by a native speaker. I think it needs the 'so' to show understanding, and not mere repetition, of the extent referred to earlier in the conversation, ie "I'm very busy."
In my example, "thank you very much" might still be too much, and "thanks" or "thanks very much" would probably be better. It depends how grateful the speaker is, and how much effort the other went to, in order to help.
I'm only a teacher, but I do enjoy thinking about how we use language with such subtle nuances. I may be quite wrong - I'm not following written rules here, I'm just trying to let you know how these words sound to me. I hope it helps you, because as it becomes clearer to me, I think I will be able to teach it better too!