Are there configuration settings to remember docked toolwindow positions in the VBE?
Yes, it is possible to configure this, but no, it has not been implemented yet. Essentially, this would involve remembering whether the dockable windows are currently displayed when the add-in is unloaded.
In order to do this, Rubberduck could store these positions in the settings file and display them when it is loaded.
If you wish, you can create an issue for this, and the team may implement it in time for the next release if it has enough support.
Full Disclosure: I am currently working on the Rubberduck Team.