Well, not always.
For example:
http://pastebin.com/kpgsBpFz
and
http://pastebin.com/uGEsNUZk
This happens to second level of variations and it's not obvious when the settings of "Keep variation in line" is set to 1 but when it's set to 2 or above then it becomes obvious.
So the second level of variation starts from a new line from the indentation of the main line and the main line continues on the same line as a "inline variation", instead of continuing from a new line (main line) and the second level of variation starting from a bigger indentation on a new line.
The main line continues on the same line of the second level of variation when "Keep variation in line" is set higher than 1 and "Column style" is not checked.
Even when the "Column style" is activated the second level of variation start from a new line form the indentation of the main line instead of a higher indentation.
I hope I didn't confused you.
Fixed in svn#1749