How to reproduce:
0. Download and extract "ScriptableBuildPipelineBug.zip"
1. Ensure `SampleProject\Library\ScriptAssemblies\BuiltinAssemblies.stamp` does not exist
2. Edit `RunSample.cmd` to change the path to the editor to your install of Unity 2018.4.1f1.
3. Run `RunSample.cmd` and wait for it to finish. The build output will be logged to `BuildReport.log` next to the `cmd` file
4. View `BuildReport.log` and see that user assemblies are compiled by looking for the log
`- Starting compile Library/ScriptAssemblies/*`
* This is normal on a first run so let's continue
5. Note that `SampleProject\Library\ScriptAssemblies\BuiltinAssemblies.stamp` does not exist
6. Re-run `RunSample.cmd` and wait for it to finish.
7. View `BuildReport.log` and see that user assemblies are compiled by looking for the log
`- Starting compile Library/ScriptAssemblies/*`
* User assemblies should not be recompiled as nothing has changed
* Note that `SampleProject\Library\ScriptAssemblies\BuiltinAssemblies.stamp` does not exist

Expected result: the BuiltinAssemblies.stamp file is generated
Actual result: the BuiltinAssemblies.stamp is not generated

Reproducible with: 2018.4.11f1, 2019.2.8f1, 2019.3.0b4, 2020.1.0a8
Could not test with: 2017.4.33f1 (the .bat file stopped at "Couldn't set project path to: SampleProject")