We can still say “write out by hand” and mean just that – that with pen applied to paper, we wrote something by hand.
But now the phrase “write out by hand” is being applied to computer contexts, namely, writing out code by hand. Now… have you ever seen anyone write out HTML code with pen and paper (other than demonstration purposes)? Hardly. And that is not what is meant when the phrase is used in this context; it simply means the code was typed out (by hand) in a text editor like TextEdit or Notepad, rather than created in a WYSIWYG program.
Even though I know what is intended when people say “write by hand ” for digital documents, I don’t think it really fits… or does it? I’m not sure yet. Just as a “book” for me is still bound paper, “writing by hand” still implies a connection to paper as well. Perhaps that’s not very next-gen-librarian of me. I think the connection implied between writing on paper by hand and writing code by hand is the labor involved in both tasks. Typing is generally believed to be better than writing (I said generally!) and using WYSIWIG programs is considered by many to be faster than coding. But there is a certain pleasure or satisfaction in doing something manually. I believe it’s one part “if you want it done right, do it yourself” and one part “do something with my hands.”