This behavior is by design: changing the build target and making a player build is not possible in the same batch mode execution as the build target change requires scripts to be reloaded.
To fix the problem, split the execution in two batchmode commands:
[PathToUnity]\Unity.exe" -batchmode -nographics -quit -buildTarget Android -projectPath [PathToProject] -logFile log1.txt
[PathToUnity]\Unity.exe" -batchmode -nographics -quit -projectPath [PathToProject] -logFile log.txt -executeMethod Builder.BuildAndroid