So apparently there is no info in regards to an error which complains about a permission issue involving cmd.exe / Build.bat. While there are basic permission issues reported, which can be resolved by running VS as admin, it won’t work in all instances.
ERRORS
|Warning||Unable to create process C:\WINDOWS\system32\cmd.exe (access denied)
|Error|MSB3073|The command C:\UE\Source-4.26.2\Engine\Build\BatchFiles\Build.bat SA_SERVER Win64 Development -Project=C:\UE\SPACEALPHA_SERVER\SPACEALPHA_SERVER.uproject -WaitMutex -FromMsBuild exited with code 6. ( ERROR_INVALID_HANDLE)
Another issue may be that the source build is not visible when you Switch your Project version to the source build, in which case you can manually assign it by clicking the 3 dots (see image).
Then was able to build with this branch, without errors.
Probable Issues preventing the Build earlier
Did not run the *bat files as admin.
Two days earlier the branch download through Setup.bat stopped several times with: Unable to connect to the remote server (WebException) - but finished successful after restarts.
While looking into the various possible issues, including reading the official instructions, the forum, AnswerHub - nowhere could I spot mention of above issue / method.