You should add ManifestDependencies entries in to your CommonSettings, specifying the paths to the manifest files for Engine and Editor localization targets within UE4 (IE: Engine/Content/Localization/Engine/Engine.manifest). This should cause any text that is part of the Engine and Editor to be excluded from your manifest.
For instance, if your project’s root directory is next to Engine:
[CommonSettings]
ManifestDependencies=../Engine/Content/Localization/Engine/Engine.manifest
ManifestDependencies=../Engine/Content/Localization/Editor/Editor.manifest
This should remove the remaining entries. If not, please let me know so I can investigate or provide an existing solution.
UPDATE: The following changelists should alleviate remaining issues with editor-only data being processed for gathering text when it isn’t desired.
2621214 Editor-only data is now gathered for localization by opting-in through a new setting.
2621217 Updated engine localization configuration scripts to use the new setting to gather text from editor-only data.
2621233 Made PinFriendlyName and relevant methods defined only in editors that have WITH_EDITORONLY_DATA evaluating as true.
2621263 Added ShouldGatherFromEditorOnlyData setting to localization dashboard UI for gathering from assets and metadata.
These should be in for 4.9, if you would prefer to wait and have the changes vetted by the 4.9 release date.