That is due to a bug in the 4.12 pre-release. It should be fixed for the official 4.12 release, but if you need it up and running now, you can change a line of code in the AutomationTool code.
Find StageRuntimeDependenciesFromReceipt in DeploymentContext.cs and change:
bool bRemap = RuntimeDependency.Type == StagedFileType.UFS && !bUsingPakFile;
to:
bool bRemap = RuntimeDependency.Type != StagedFileType.UFS || !bUsingPakFile;