Great job with this script.
EDIT UPDATE
@matortheeternal
Thank you for the update.

So far I was able to successfully merge:
MERGED
===========================================================================
Atlas Map Markers.esp v1.64 Scripts present
Atlas Blackreach.esp v1.0
Atlas Dawnguard.esp v1.23 Scripts present
Atlas Dragonborn.esp v1.0 Scripts present
Merged file Test:
Merged file name: Atlas Map MarkersM.esp-->Atlas Map Markers.esp
TES5Edit Apply Script - Check for errors = 
Playing on an existing save = 
New game save = 
===========================================================================
Warburg's 3D Paper World Map - Texture 3.esp v3.3
Warburg's 3D Paper World Map - Dawnguard.esp
Warburg's 3D Paper World Map - Dragonborn.esp
BSA
Warburg's 3D Paper World Map - Texture 3.bsa (no player marker)
Warburg's 3D Paper World Map - Dragonb.bsa
Merged in one file xxx.bsa with BSAopt 64bit
rename to Warburg's 3D Paper World Map - Texture 3.bsa
Personally I always unpack BSA from mods, people often pack a lot of junk out there: *.db *.txt ...
I do not Unpack BSA from "Warburg's 3D Paper World Map" as loose files.
This applies only to this particular modification.
In the BSA, there is a terrible mess. nearly 90 percent of the content of the BSA is not used by modification.
Unfortunately, because of the mess in the BSA
It is difficult to get what is needed and what is not. (and the modification does not work properly)
Merged file Test:
Merged file name: Warburg's 3D Paper World Map - Texture 3M.esp-->Warburg's 3D Paper World Map - Texture 3.esp (Load Order ALWAYS ON THE VERY END, Even after Bashed Patch, 0.esp, Reprocer.esp etc...)
TES5Edit Apply Script - Check for errors = 
Playing on an existing save = 
New game save = 
===========================================================================
Supreme Storms 1.2
Supreme and Volumetric Fog 2.0
Option 1
Supreme Fog.esp
Supreme Storms.esp
Merged file name: SupremeFogAndStormsMERGED.esp (Load Order above ClimatesOfTamriel-Sound.esp)
Option 2
Supreme Fog - CoT.esp
Supreme Storms - Cot Version.esp
Merged file name: SupremeFogAndStormsCoTMERGED.esp (Load Order after ClimatesOfTamriel-Sound.esp)
Option 3
Supreme Fog.esp
Supreme Fog - CoT.esp
Supreme Storms.esp
Supreme Storms - Cot Version.esp
Merged file name: SupremeFogAndStormsCoTMERGED.esp (Load Order after ClimatesOfTamriel-Sound.esp)
Merged file Test: (all option)
TES5Edit Apply Script - Check for errors = 
Playing on an existing save = Currently testing.
New game save = Currently testing.
===========================================================================
Cloaks of Skyrim v1.2
Cloaks.esp
Cloaks - Dawnguard.esp
Merged file Test:
Merged file name: CloaksM.esp-->Cloaks.esp (Load Order the same as the Cloaks.esp)
TES5Edit Apply Script - Check for errors = 
Playing on an existing save = Currently testing.
New game save = Currently testing.
===========================================================================
Improved Closefaced Helmets v0.9
imp_helm.esp
imp_helm_dawn.esp
imp_helm_night.esp
File imp_helm.esp contains errors (I do not know whether they are the result of error or deliberate action)
[00:00] Checking for Errors in [03] imp_helm.esp
[00:00] Weight slider - Female -> <Unknown: 2>
[00:00] Above errors were found in : DNAM - Data
[00:00] Above errors were found in : DwarvenHelmetOrc [ARMA:030096A3]
[00:00] Weight slider - Male -> <Unknown: 0>
[00:00] Above errors were found in : DNAM - Data
[00:00] Above errors were found in : DaedricHelmetAA [ARMA:00098BB2]
[00:00] Weight slider - Female -> <Unknown: 2>
[00:00] Weight slider - Male -> <Unknown: 2>
[00:00] Above errors were found in : DNAM - Data
[00:00] Above errors were found in : DwarvenHelmet [ARMA:0003F7FF]
[00:00] Above errors were found in : GRUP Top "ARMA"
[00:00] Above errors were found in : [03] imp_helm.esp
cleaned errors

Merged file Test:
Merged file name: imp_helmM.esp-->imp_helm.esp (Load Order the same as the imp_helm.esp)
TES5Edit Apply Script - Check for errors = 
Playing on an existing save = 
New game save = 
===========================================================================
I noticed that after the merge
Purewaters.esp v4.4
PurewatersDG.esp v4.3
PurewatersDB.esp v4.3
(optional if you use RND)
RND_PureWaters-Patch.esp v1.9.5

Not everything was ok, but merge files only from Purewaters works ok.
The same is true for both versions of the script.
Merging without script produces the same results.
Edited these records manually.
Merged file Test:
Merged file name: Purewaters.esp,PurewatersDG.esp,PurewatersDB.esp,RND_PureWaters-Patch.esp
(Load Order the same as the Purewaters.esp
)
TES5Edit Apply Script - Check for errors = 
Playing on an existing save = 
New game save =
===========================================================================
It would be good to put info on the main page in the "Tutorial",
after loading the files to TES5Edit check first "check for errors"
(the script can check loaded files for the presence of bugs (errors)?)
sorry for the wall of text 
Edited by insaneplumber, 30 August 2013 - 06:27 PM.