Problem was coming from the -nographics commandline argument. As part of the player build, the editor tries to generate the sky ambient probe and reflection probe. That computation requires a gfx device to be loaded otherwise the probes were simply filled with uninitialized data.
Solution is to either run the player build without -nographics or to generate lighting in the editor for each scene included in the build (no need to add lights or generate lightmaps, simply hitting generate lighting will bake the sky probes).
Also the application logic was modified to not attempt to render the probes when -nographics is set.