It is consensus that with the exception of inline citations (and similar templates) each parameter stands with leadin pipe on a new line. At this time the CTT removes all line breaks and spaces before and after pipes as well. The necessarity of edits like this is kind of annoying.
It is also consensus (at least in DE:WP) that for inline used templates there is a space in front of the pipe, as it makes reading and navigating within the source text more easily. CTT removes those "leading" spaces.
I guess this is rather a Visual Editor bug/problem.