BigMaps cannot perform such a function as I had described. I don't see it ever will.
From the Bethesda Softwork games, beginning with Morrowind for the Elder Scrolls on up, non-specified cells (cells being their name for in-game maps that generally link together) were given the EditorID "Wilderness" as a timesaving measure. This allowed the creators to focus more upon the more distinct and quest/goal specific areas such as "SeydaNeen02", "SkingradExterior02" or "DLC1VampireCastleExterior05" (yep, Castle Volkihar).
Bethesda Softwork's prior Elder Scrolls games, Arena and Daggerfall, gave a false sense of scale. By that, no actual foot-travel between landmarks (cities, shrines, dungeons) was possible and only performed within the Travel Map. Each city/dungeon/etc map was standalone and fitted with a map-looping system where one could walk endlessly, or reverse course to return to the place they left. There was no actual world map to traverse, and it was a simplified means to simulate its grand scale.
However, the individual Wilderness cells within these games are themselves unique and not reused. While they are given the EditorID "Wilderness", every individual cell within their related games have unique Hexadecimal FormIDs separating one from another. And within the editors, you would not merely see the EditorID and Name of the Map, but a specific X/Y coordinate where it is placed within its "WORLD", its version of BigMaps.
In the Editor for Oblivion, the "World Space" named Tamriel has hundreds of individual cells, the bulk of which all have Wilderness Editor IDs, though each is its own unique cell with its own unique FormID. The cell for Malacath's Shrine is located at (-50, 2). However, each surrounding cell is a unique Wilderness cell (-50,3), (-49,2), etc.
Yes, I've done some TES modding. I assisted a friend with a project where houses of 'dead/killed' NPCs could be purchased; all 'respawning' items replaced with non-respawning... static damaged walls and boarded up windows/doors replaced or repaired (Dark Brotherhood Sanctuary for one... you wouldn't believe the job!). Not sure when its going on Nexus.
When one creates a mod for any of these games, they would be placing within their desired cell (wilderness or not) new reference objects, be they NPCs, static objects such as a new house, castle wall, or activator objects such as teleport centers or shrines. It would drive one creating mods nuts if the maps were randomized, or duplicated.
A unique shrine to the MLP Unicorn Daedra (they are all evil) being placed within MAP 13 (your example) would not be so unique if Map 13 was reused in two areas. And for BigMaps, the system does need to fall back upon the individual MapIDs for features such as Teleport. Wishing to teleport to Map 13 at coordinates 3,6 would be tricky if there were indeed two Map 13s pasted together. I know you would say that, as a game developer, you wouldn't establish any unique items in a dup map, but I am hoping to make modding possible.
I cannot say for Neverwind Nights system, but I know that there is no map/cell duplication within the Bethesda Softwork games since the 90s, and BigMaps would have issue.
Now, as towards the 999 map limit, there are scripts to break that. But I have never checked them out, nor do I know compatibility with them. I suspect manual editing of the map files (or MapInfos file) would be needed if in use. But again, I never used any that broke the map limit, and could not guarantee compatability... BUT THAT WOULD BE AWESOME.