Why try to write code when BleST will do it for you.

https://i.imgur.com/gc2GWUM.png

My take from what your asking:

The different linked models objects are the same (ie, cube1 is exactly the same as linked cube2)

and the UVs islands are unwrapped the same for these linked objects (the UV islands of Cube1 are exactly the same as the islands for Cube2??)

and you want these linked objects to use different skins via UVMaps or is this happening now?

Questions:
Are these linked objects in separate blend files (as in the old link/append objects between blend files) or are they linked duplicate objects (using Alt+D, I think it is) in the same Blend file?

You want this to happen where, In Blender so you can see the skins in Blender or in Portal2 after export?

If Portal2, this is all QC/VMT work based on Blender material names as far as I know. There is no direct tie to textures from Blender in a Valve Model. The object name, UV layout and material name are baked into an object (smd/dmx) on export.

Maybe I'm totally off base to what your asking here so maybe a couple of marked up screen shots of the objects/project might make this clearer because I'm not following what you're trying to ask.

And this may be totally irrelevant to what your trying to ask and you know all this already but I'm trying to help based on what has been asked and my interpretation.

Yes this is image is Pre-Blender 2.8x and is directed at people trying to port models to SFM, but the links from Blender to the Valve Material System are still the same in all versions of Blender.

https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=1528003376

As far as I know, Valve models don't support multiple UV maps. It's all done through $Bodygroups or $texturegroups. (I could be wrong!)

https://steamreview.org/BlenderSourceTools/archives/

Do not decompile the TF2 Characters from game. There is something that screws up the legs when creating animations in blender and pass them back to SFM.

You should use the SDK Reference models found in the SourceSDK.

In the VPK folder for the SourceSDK program, you find "depot_211_dir.vpk" and extract a folder called sourcesdk_content. It can go anywhere on your computer.

Inside that folder you'll find a folder called TF and inside that folder a modelsrc folder then inside that a player folder.

This is where the pure reference models reside in DMX, SMD and Maya formats. These are the player models you should use for creating animations.

To get the Source SDK you need to go into your Steam Client Library, select TOOLS and install the "Source SDK" tool (Not to be confused with the Source SDK Base Tools).

https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2012405066

In that picture, the models that are "Spaced Out" are using decompiles of the TF2 game player models.

The aperature scout was created from the SDK reference models and the animation works fine on it in SFM.

Did you set up the export folder, and game path to the game studiomdl verison you're exporting the model for in the BleST screens?

yup, you're using SourceIO for this, you need to talk to RedxEye about this via his GitHub...

In the error...

"SourceIO\source2\blocks"

Did you select everything including the armature and press Ctrl+A - Apply All transforms before exporting?

Before exporting the SMDs, do a Ctrl+A and apply all transforms, then export the SMDs.

https://steamhost.cn/steamcommunity_com/sharedfiles/filedetails/?id=2504104433

What you're looking at there maybe the sky boxes. Hide the top or side planes of the the big one and look inside or put the model in to wireframe mode and see what you find inside them.

Hmmm. then again I downloaded your blend file and all there are are angled planes inside.

Is the map supposed to look like those 3 stacked cubes without anything inside them?