This looks interesting I was doing this in a different manner by manually deleting excess zones/zone_points/doors ect things all tied to the specific zones that wouldn't be used. I kept some things just in case like quest's, npc's, and items since I might want to alter them a bit to reuse them.
After I deleted what I wanted I'd save the DB table's in SQL patch folders I made for different categories SQL Create, SQL Drop, and SQL Drop/Create. Then I could just access MySQL DB in cmd use the DB of choice and source in or out what I wanted as needed. There is probably a easier method to do it like what you suggested, but that's just the way I was able to figure it out personally like you I'm still learning.
Also all the various SQL patches I named accordingly in a way that made some to myself. You can just overwrite update them as needed as you make changes. You could also make a new SQL for those tables and place the older versions or alternate ones of those tables in a backup folder as you develop them. Then you could change and or revert to whatever one you liked later by sourcing the patches back into the DB at any time.
Like you I'm a fan of minimalism and being able to remove unneeded and unused clutter from my server DB keeping more compact in size. It has practicality merits though as it saves on your overall system memory that could be used to host more static_zones for example or to insert more overall spawn and player related stuff inside your zones and db in general.
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