Steps to reproduce:
1. Open attached project
2. Build scene in developer mode and attach Profiler
3. Launch build and observe profiler spikes
4. If you run same scene in editor, there are no spikes

Expected result: The spikes should show up in both the editor and the build
Actual result: The lag spikes are visible only in the build

Reproduced on 5.4.0p4, 5.5.0f3, 5.6.0f3, 2017.1.0b1

The stall is caused by a blocking readback from GPU of the generated skybox texture when generating input lighting for the dynamic GI system.

The workaround in 5.6 and older is using an animated color value for the GI that is an average value of the skybox, this was done by hand for the courtyard project https://blogs.unity3d.com/2015/11/05/awesome-realtime-gi-on-desktops-and-consoles/
https://www.assetstore.unity3d.com/en/#!/content/49377

In 2017.1 there is an API for setting the full environment data yourself: https://docs.unity3d.com/2017.1/Documentation/ScriptReference/DynamicGI.SetEnvironmentData.html