In ST 2.0 I had a list with pull-to-refresh plugin above it, and also another simple plugin written by me (basically a search field) above the list items and below the pull-to-refresh. My plugin scrolled "nicely" with the list items and pull-to-refresh.
After upgrading to ST 2.1, I couldn't adapt my code to display a container between pull-to-refresh and the list items, which also scrolls nicely as before.
This thread suggests a solution using the scrollDock config (not documented even as a private member). However, my list has headers, so a container with scrollDock set to 'top' is placed above the first item but below the first header.