How to reproduce:
1. Open the "SampleScene" Scene in the attached "case_1154609.zip" Unity project
2. In the Project tab, select the "sfm" Asset and change its settings in the Inspector tab
3. Apply the changes and observe the Hierarchy tab

Expected result: settings are applied without creating empty GameObjects
Actual result: empty GameObjects are created in the Hierarchy tab

Reproducible with: 2018.4.1f1 (package ver. 0.1.2), 2019.1.5f1 (package ver. 1.0.0-preview.2), 2019.2.0b4 (package ver. 1.0.0-preview.2), 2019.3.0a4 (package ver. 1.0.0)

Note: only reproducible with an Alembic file that does not have an Imported Object. Different package versions work on different versions of Unity: the issue can be reproduced on Alembic version 0.1.2 or later and Unity versions 2018.3.0a6 to 2018.4.1f1 and 2019.1.0a1; Alembic version 1.0.0-preview.2 or later and Unity versions 2019.1.5f1, 2019.2.0a2, 2019.2.0a3 and 2019.2.0b4; Alembic version 1.0.1 or later and Unity versions 2019.2.0a4 and 2019.3.0a4. The issue cannot be reproduced on versions 2018.3.0a5 and earlier because of errors preventing Alembic file editing. The Alembic package is compatible with Unity Editor 2018.1 and later.