I’m also using a Deployment process including 3 environments. This is an issue we can’t really address automatically unless you check the difference between 2 sql dumps I guess.
The way to go would be to create a bit of PHP to populate your settings on deployment (or on plugin activation). It’ll obviously involve to check the plugin source code and/or the database for the options table.
Unfortunately I’m not aware of any solution which would help with that otherwise.
(Considering you are already using something like WP_Skeleton & WP_Stack)
Hope that helps