How to reproduce:
1. Open the attached project ("case_1174117-AddressablesTest.zip")
2. Open the repro scene ("SampleScene")
3. Set "Packed Assets" asset's bundle mode to "Pack Separately"
4. Set "Play Mode Script" to "Packed Play Mode"
5. Build Player Content
6. Enter Play mode

Expected results: No warnings in the console, dependency chains are resolved correctly
Actual results: Warnings in the console about missing script references, dependency chains fail

Reproducible with: 2018.4.6f1, 2019.1.14f1, 2019.2.1f1, 2019.3.0a11
Couldn't test with 2017.4, as it does not support Package Manager
Not reproducible with: 2019.3.0a12
Reproducible with package version: 0.8.4, 1.1.7

Notes:
1. Couldn't reproduce this issue when "Play Mode Script" was set to "Fast" or "Virtual" modes
2. Couldn't reproduce this issue when bundle mode is set to "Pack Together"