Recent change notesVersion 1.0.0 (Build 5)
General usage instructionsWindow -> Tool Window Management -> Configure Preferred Availabilities...
opens a dialog listing all of the tool windows registered for the current project. Cells in the right-hand column may be edited to express your preference for the corresponding tool window's button availability. Buttons are made (un)available on committing the dialog. Select "None" to have a tool window revert to its default availability.
Other menu choices are available to reapply your preferences and restore the default availabilities.
Note that the plug-in can't prevent buttons becoming (un)available (it wouldn't have been possible to implement otherwise...) so be prepared to reapply your preferences should the need arise (perhaps binding the action to a keyboard shortcut for convenience).
Settings are stored in the project's .iws file and are applied "shortly" after the project is opened. It's impossible to determine the point at which the project and all other plug-ins have finished initialization (including registering their own tool windows), or to detect new tool window registrations so, unfortunately, it can't be guaranteed that your preferences will (all) be applied after a project is opened.