It's perfectly possible to create a new map for a custom/mod added Worldspace.
The cartographic process is however somewhat involved:

Phase I - Imaging the Worldspace
- Create an overhead rendering of the target worldspace (satellite map)
- Crop the render as required and save it as DDS, this is gonna be the map texture
- Save another DDS copy, and near top left and bottom left right corners of the map texture, draw a red dot or cross in that copy
- This copy with the red dots will be our cartography texture
- Edit the target worldspace mod to use the catrography texture (with the 2 red dots/crosses) as the worldspace map

Phase II - Measuring the Worldspace
- Load game with target worldspace mod, move player character to target worldspace
- With your character, visit the top left, and and the bottom right corner of the worldspace and for every corner:
-- Use the ingame map to localize the red dot or cross position for the corner as best as you can, with your character. Stand right on top of 'em dots and always rotate your player char to face North before reading coordinates.
-- Once located, use console to obtain X and Y coordinates of player character.
-- For top left corner, note down Top=<insert Y coordinate of PC> and Left=<insert X coordinate of PC>
-- For bottom right corner, note down Bottom=<insert Y coordinate of PC> and Right=<insert X coordinate of PC>
- From the target worldspace mod, obtain the worldspace record id and the filename of the mod, note both down

Phase III - Mapping the Worldspace
- Create a new plugin that has the map plugin (ESL) as master. In this new plugin:
- create a new copy of LSM_MAP_Commonwealth Activator and rename it
- Edit the SettlementMap:MapScript script properties on the new Activator:
-- Edit MapWorldspaceDefinition property
---Edit description property to say something like "My Awesome Worldspace"
-- Edit FormID property to reflect the worldspace record id you noted down
-- Edit pluginname property to reflect the mod filename you noted down
-- Edit the WorldBounds Property to reflect the coordinates you noted down (Top, Bottom, Left, Right)
-- Save the script edits

Phase IV - Preproduction
- In the new plugin:
-- Create a new Constructible Object for the new map Activator you copied and edited (best to copy and edit an existing one)
-- It may be necessary to edit some conditions on the COBJ, I don't remember.
-- Create a copy of the SM_Commonwealth.nif and it's material file SM_Commonwealth.bgsm and rename them
-- Edit the material file to use your catrography texture as diffuse.
-- Open the nif in nifskope and find the TopLeft and BottomRight NiNodes.
-- Edit the TopLeft node Translation property so that the node sits exactly over the red dot in the top left corner of your cartography texture
-- Edit the BottomRight node Translation property so that the node sits exactly over the red dot for the bottom right corner.
-- Edit the path of the MapTriShape's LightningShaderProerty material, so it matches your newly created and renamed bgsm
-- Configure the new map Activator to use your newly created nif as the map model

Phase V - Production & QC
- Edit the material file to use the map texture you made way earlier as diffuse
- In the target worldspace mod, set the target worldspace to use the map texture as the worldspace map
- Load game with mods
- Double check that the mod with the target worldspace does actually have workshop system registered settlements in it
- Build new map
- Verify that the coords of settlement indicators (lamps) spawned on the map  are on spot


Done. Enjoy!