The reliable two–way sync is simply not something that have happened in WordPress.
The typical way is in line with what you are doing — pulling a copy of production database into development environment. Note that this is commonly the one direction it goes. It’s much more problematic to try sync development back to production.
As far as plugin configuration specifically is concerned:
- Call it good enough and treat production as authoritative state
- Have codified install/update procedures, which dictate desired state of plugin options
- Override plugins’ options storage and/or internal hooks
The practical choice to go with would depend on specific plugins used and how complicated the state of their settings to be captured and/or reproduced is.