The issue with scripts came up when Sierra was still in beta, because AS pre-10.12 still included resource fork stuff when saving, even though it was no longer needed. So at that stage you couldn’t codesign from SD or SE.
Changes were made to AppleScript so that resource forks are no longer included in saving. But if you add, say, a script saved under 10.11 (say, a library) into a bundle and try to save and sign it in SE under 10.12, you still get the error. We decided it made more sense for SD just to strip them immediately before codesigning.