Generally, a newly created note will open just below the note where the cursor is - if the cursor is in a note.

But if
I have a number of notes in a given document and
place the cursor in the bottom-most note and then
switch focus to the Editor,
a newly created note will open at the top of the column.

Is this intended?

For me anyway, I'd prefer to have the new note open at the bottom of the column, so that its position (usually) will track the position of the corresponding key in the text.

Yep, we'll pick this up and fix it in a upcoming release!