So, the Mongols were the first to use what is known as topological map in their military operations, but in mapping your Sandbox, what you are doing is beyond topology.
Let me explain. I knew a guy very long time ago. He wrote a novel, based on his experience playing the famous A-series of the AD&D Modules. He freely wrote of the Magic Users and Rangers, and of the events in those modules. You know, what the problem with his novel was? He could never publish it as his own work, make money off it or gain recognition - it was all TSR's copyrighted material. TSR's logo, "Products of your Imagination" took on a new and sinister meaning for me.
Let's say you run a D&D game or an OSR clone. You set it in Forgotten Realms, or in the Dark Sun, or in a dozen other commercially available settings. Let's say you find an adventure you like and a bunch of pre-generated NPC's from a supplement you got off e-bay. None of it is your stuff. Every DM I know, customizes every game product to fit their unique fantasy world. What OSR Renaissance really consists of is a bunch of would be Gygaxes creating their own campaign settings, but using someone else's game mechanics under the open license system.
So, the task before any DM is to separate the wheat from the chaff, their unique world from what they borrow from others, so that ultimately, they can develop and publish their own unique ideas. What follows next is to make the topological map of your sand-box. Take elements and images that make up your own unique setting, fantasy, story, and put them on paper, connect them, as it would make sense in a story or a movie.
I know what is in my Midlands setting - my love of landscapes, man-made and natural, some years of field reconnaissance in the military, my love of the wilderness adventure, mystery, mysticism, indecipherable alien artefacts. This is what my map looked like, a list written on a piece of paper:
BLACK OILY SEA
My next map was of the Barony, the base for the players:
GREAT WHITE FOREST (Birch Forest)
SEA OF FLOWERS , RIVER HOB, BLACKLANDS BARONY, SATILLA RIVER, LEONSFORD
(Mad Wizard Turf) (Barony)
BURNED LANDS (Burnt forest) South of the Blacklands Barony
100 MILES OF FOREST
DESERT WASTELAND (Demon Coast North Frontier)
After that I drew a regular topographic map of the Barony and its outlaying areas.
I had thought about the Midlands setting for two years or so, before putting it on paper. To show how to map the Sandbox, I will use the example of a sci-fi story I worked on over 30 years ago, and will use the mapping process to make an RPG setting for it:
CENTRAL CONCEPT: Forest on the edge of the desert with hard wind blowing through mighty trees all the time. Local scavengers (humans) make webs of the steel wire strung across the trees to catch stuff - junk and artefacts blown by the wind.
Desert hides an old battlefield
Spider scavenger forest is in the foothills among the crags and canyons channeling the desert wind.
CONCEPT: Space travel experience is piloting by instruments - combination of the WW2 Submarine and the Flying Fortress experience.
Pirate Spaceship Marooned or Laying Low in the Area
Bearded Captain lives in the bridge area of the ship.
His crew camps in the tent camp outside, sheltered from the wind
A spider scavenger human outcast lives in a hut surrounded by rusting equipment. He checks his webs periodically.
Sparse other Scavenger homesteads in the area
MAD MILLER - NPC - Imperial Biologist, lives alone in the maze of wind blown sand stone canyons.
His wife divorced him because he wouldn't grow up.
You navigate the windblown desert in rusty old tracked tractors covered with sheet metal, called Crawlers
Scavenger NPC has a crawler rusting in his yard.
BEASTIES - sentient native animals living in the canyons on the edge of the desert. Miller knows they are intelligent and does not report them to his superiors as he should.
BEASTIES friends with and protect Mad Miller.
Hunting intelligent beings is an illegal sport.
Miller was going to guide a hunter of intelligent creatures to make a lot of money to get off the world and start a new life, but changes his mind.
BEASTIES trusted Miller and his friends in their total innocence, Hunter was a degenerate about to murder them with his firepower, but Miller murdered him in the fit of conscience.
Miller dragged the body, as well as all of the gear and evidence onto the hunter's ship, and then programmed the autopilot to accidentally fly into an asteroid belt at high speed, thereby erasing his tracks.
As you can see, this is a brainstormed story with coalescing Traveler adventure/setting elements. There are NPC's, Places that can actually be mapped, and possible story hooks:
Wife wants to get Miller back of wants players to escort her to him.
Hunters family hired players to solve the mystery of his disappearance.
Players hunting the Pirate Captain.
Players Marooned on the World.
Players are Pirates' prisoners forced to escape.
Players are treasure hunters, need to explore desert, they did not know was inaccessible due to sand storms.
One thing to keep in mind - if your adventure map is your sandbox, and there are no foreign elements, say, from another setting. If the players are not traversing a topographical map, but a topological map of your story, then they can not throw your game by refusing to go into your dungeon, because they are effectively IN your world from the beginning.
I have no problem with topographic maps, and use the other maps for mapping the social terrain, make node maps for social encounter based adventuring. My players can literally go anywhere they like, crossing the geographic map as a tabletop game, while also navigating the topological map of the story that the DM secretly keeps track of.