Ones tiny and between two other links. The other is quite large and all by itself.
I don't see a problem here. The (link/edit/close/flag) toolbar need to stick right close to the actual text of the question and tags, because they are pretty much meant to act on that (ok, the link button could go elsewhere).
The "add comment" should stay separate from those tools - it's not about changing or flagging the question. And it makes a lot of sense where it is when there are comments already - you're kind of replying to, or adding to, the comments above it.
When there are no comments I still think it's good to have it where it is. Posting a comment is more link proposing an answer in the sens that you're giving input. So it's good that it's closer to the "answer" part than the "question" part.
Moving the toolbar to the right above the flair would make it much less obvious/harder to locate in my opinion. And it would waste vertical space, which comes at a premium. (I'm guessing even more so on mobile devices, but I have no idea what the layout is on mobiles).
So: no thanks.
Now inverting the flair and the toolbar (flair on the left, toolbar on the right) would be fine with me, no issue about that. I don't really see what it would gain though. But in that case I'd move the "add comment" link with the toolbar though, not leave it on the right - it would be even less obvious all alone below the flair, and would look like you're leaving a comment on the user rather than the question. So I'm guessing you wouldn't like it for the same reason - same relative layout. (Squishing the "add comment" between the question and the flair would be even worse.)
I'm not even considering a scheme where you'd move the flair to the top of the question and have the question contents flow around it (left or right). That would allow to have the toolbar bottom left and the comment to the right (or the opposite), which I am thinking you would rather have. But that would make editing the question a pain if you need some code or fix format data near the top.