First of all, double check port for adonix, it must be different from main runtime port. As a second thing, what version of MSSQL do you have right now, anything older then MS SQL 2016 is not supported. As far as I can see, you are using unsupported version of MS SQL (2012).

Thanks for this feedback ! Indeed I had version 2012 (11.3.6020). I migrated it using the option standard migration feature to version 2019 (15.0.2000).

However I still get the same issue:

1/18/2021 4:48:09 PM : INFO  - 
1/18/2021 4:48:09 PM : INFO  - ---------------------------------------------------------------------
1/18/2021 4:48:09 PM : INFO  - Sage Application setup 1/18/2021 4:48:09 PM
1/18/2021 4:48:09 PM : INFO  - ---------------------------------------------------------------------
1/18/2021 4:48:09 PM : INFO  - Starting application configuration
1/18/2021 4:48:09 PM : INFO  - 
1/18/2021 4:48:09 PM : INFO  - *--- Sage Application setup ---*
1/18/2021 4:48:09 PM : INFO  - Application : reading adxinstalls on localhost...
1/18/2021 4:48:09 PM : INFO  - Information from adxinstalls.xml on application server retrieved.
1/18/2021 4:48:09 PM : INFO  - Ok
1/18/2021 4:48:09 PM : INFO  - Database : reading adxinstalls on localhost...
1/18/2021 4:48:09 PM : INFO  - Information from adxinstalls.xml on data server retrieved.
1/18/2021 4:48:09 PM : INFO  - Ok
1/18/2021 4:48:09 PM : INFO  - Information from adxinstalls.xml retrieved.
1/18/2021 4:48:09 PM : INFO  - Ok
1/18/2021 4:48:09 PM : INFO  - Main runtime : reading adxinstalls on localhost...
1/18/2021 4:48:09 PM : INFO  - Information from adxinstalls.xml on main runtime server retrieved.
1/18/2021 4:48:09 PM : INFO  - Ok
1/18/2021 4:48:09 PM : INFO  - Reading solution.xml on localhost...
1/18/2021 4:48:09 PM : INFO  - Information from solution.xml retrieved.
1/18/2021 4:48:09 PM : INFO  - Ok
1/18/2021 4:48:09 PM : INFO  - Starting configuration from Runtime SAFEX3RUNTIME, localhost:
1/18/2021 4:48:09 PM : INFO  - File c:\Sage\SAFEX3APPLICATION\folders\X3\X3APPLI.ini retrieved from localhost. (LibAdm.GenerationScriptsAppliNT)
1/18/2021 4:48:12 PM : INFO  - Database schema X3 is available and storages are online (LibAdm.RunVerifSchemaBaseSqlServer)
1/18/2021 4:48:12 PM : INFO  - User for folder X3 exists, it will not be created. (LibAdm.GenerationScriptsAppliNT)
1/18/2021 4:48:12 PM : INFO  - Creation of sagex3_CrUsr.bat done. 
1/18/2021 4:48:12 PM : INFO  - Creation of _adxmainfil.bat.
1/18/2021 4:48:13 PM : INFO  - Tables list from FILPLAT in main folder created. (LibAdm.GenerationScriptsAppliNT)
1/18/2021 4:48:14 PM : INFO  - Tables list from FILPLATSYS in main folder created. 
1/18/2021 4:48:14 PM : INFO  - Creation of _adxmainfil.bat done.
1/18/2021 4:48:16 PM : INFO  - File c:\Sage\SAFEX3APPLICATION\folders\X3\X3APPLI.ini sent on application server localhost.
1/18/2021 4:48:16 PM : INFO  - File c:\Sage\SAFEX3APPLICATION\folders\X3\FILPLAT\sagex3_CrUsr.bat sent on application server localhost.
1/18/2021 4:48:16 PM : INFO  - Launching sagex3_CrUsr.bat ... (LibAdm.RunCreateUserSQLMainNT)
1/18/2021 4:48:18 PM : INFO  - Execution of sagex3_CrUsr.bat done.
1/18/2021 4:48:21 PM : INFO  - Database schema X3 is available and storages are online (LibAdm.RunVerifSchemaBaseSqlServer)
1/18/2021 4:48:30 PM : INFO  - Valfil test performed with success.
1/18/2021 4:48:30 PM : INFO  - Database sagex3 loading... 
1/18/2021 4:48:30 PM : INFO  - 778 tables found
1/18/2021 4:48:30 PM : INFO  - 0038 tables loaded - 05% - AABREV - ACLBSYS
1/18/2021 4:48:47 PM : ERROR - Error No 76

[Microsoft][SQL Server Native Client 11.0][SQL Server]The CREATE UNIQUE INDEX statement terminated because a duplicate key was found for the object name 'X3.ABITRAUNV' and the index name 'ABITRAUNV_ATV0'. The duplicate key value is (MFGCOST, MFC1-MFGCSTPE

1/18/2021 4:48:47 PM : WARN  - Warning ! Following group or table could not be loaded into database : 0000-AABREV-ACLBSYS. (LibAdm.RunValFilMain)
1/18/2021 4:48:47 PM : INFO  - 0076 tables loaded - 10% - ACLOB - ADOVALHIS
1/18/2021 4:50:20 PM : INFO  - 0114 tables loaded - 15% - AELT - AMAINT
1/18/2021 4:50:35 PM : INFO  - 0152 tables loaded - 20% - AMEMO - APLLCK
1/18/2021 4:51:05 PM : INFO  - 0190 tables loaded - 25% - APLSTD - ASHWMET
1/18/2021 4:51:50 PM : INFO  - 0228 tables loaded - 30% - ASHWOPT - AVIEWE
1/18/2021 4:52:55 PM : ERROR - Error No 76

[Microsoft][SQL Server Native Client 11.0][SQL Server]The CREATE UNIQUE INDEX statement terminated because a duplicate key was found for the object name 'X3.ATEXTRA' and the index name 'ATEXTRA_AXX0'. The duplicate key value is (AVOLUME, DES, CHI, zSVG,  

1/18/2021 4:52:55 PM : WARN  - Warning ! Following group or table could not be loaded into database : 0005-ASHWOPT-AVIEWE. (LibAdm.RunValFilMain)
1/18/2021 4:52:55 PM : INFO  - 0266 tables loaded - 35% - AVOCAB - AYTLINES
1/18/2021 4:53:09 PM : INFO  - 0304 tables loaded - 40% - AYTMEN - CCMACTION
1/18/2021 4:53:20 PM : INFO  - 0342 tables loaded - 44% - COMPANY - EDIFRM
1/18/2021 4:53:34 PM : INFO  - 0380 tables loaded - 49% - EDIMSG - EMPLOCTRSTG
1/18/2021 4:53:48 PM : INFO  - 0418 tables loaded - 54% - EMPLOCTRUKI - GACCOUNT
1/18/2021 4:54:03 PM : INFO  - 0456 tables loaded - 59% - GACCOUNTA - HRDESCTRCOT
1/18/2021 4:54:21 PM : INFO  - 0494 tables loaded - 64% - HRDSCFCY - HRDSNDMV5
1/18/2021 4:54:33 PM : INFO  - 0532 tables loaded - 69% - HRDSNDMV6 - HRTAXCERTDED
1/18/2021 4:54:45 PM : INFO  - 0570 tables loaded - 74% - HRTAXCERTINC - PARSTOACC
1/18/2021 4:55:01 PM : INFO  - 0608 tables loaded - 79% - PARTRZL - PRTSCRWRK
1/18/2021 4:56:22 PM : INFO  - 0646 tables loaded - 84% - PRVCLOB - SNPOPEAFF
1/18/2021 4:56:34 PM : INFO  - 0684 tables loaded - 88% - SPREASON - TABSAFSTO
1/18/2021 4:56:47 PM : INFO  - 0722 tables loaded - 93% - TABSDHTYP - TMPSRPTDET
1/18/2021 4:57:26 PM : INFO  - 0760 tables loaded - 98% - TRAINER - AECLIDBG
1/18/2021 4:57:52 PM : INFO  - Database sagex3 loaded in 00:09:31.4300320
1/18/2021 4:57:52 PM : INFO  - Launching X3_misc.sql. (LibAdm.LaunchMisc)
1/18/2021 4:57:54 PM : INFO  - c:\Sage\SAFEX3APPLICATION\folders\X3\FILPLAT\X3_Misc.sql executed.
1/18/2021 4:57:54 PM : WARN  - Error(s) detected in sagex3 database loading. (LibAdm.RunValFilMain)
1/18/2021 4:57:54 PM : FATAL - Configuration aborted
1/18/2021 4:57:54 PM : FATAL - ERR_CHECK_VALFILS

For Apache, the port is 80.

For the Runtime, I guess the port is 20100.

Is there any other port for Adonix ? I don't see any other port in the configuration from the console.

Then as a last question to double check is to have clear SQL database, without anything within it. Could you try to start configuration of solution from blank page to make sure that you are not missing anything. BTW, this usually means you need to install new database server component.

I found the way to reinstall DB and Runtime components... (rename old component folders, and reinstall with new names).

Note, after updating the DB to 2019 version + reinstalling these 2 components, the app installation went all good.