I think the create thread button should be on the same line as the breadcrumb ( Default position in all forums). now it shows below the breadcrumb in parent forums. and normal position in child forums.. this could be confusing for users.
The create thread button is identical to the normal create thread button, it just adds an overlay. The aggregate threads options might be pushing bits out of alignment, but this depends on your theme
You are right Xon, I have just discovered its the default position in XF. it was annoying me because of the extra space. I have followed instruction in this thread: https://xenforo.com/community/threads/post-new-thread-button.75676/
To make it look like the button in other forums.