I found the answer: It simply can be overridden per project by manually creating a DefaultLightmass.ini file in the Project Config directory. Fill with for example
[DevOptions.PrecomputedVisibility]
PlayAreaHeight=600
It actually is described in the ini file comments itself. But I believe, it would be better, if this was described in the docs here as well, which only mention to edit the Engine wide ini file (which I did without reading all comments)
I did come on this idea when playing with Device Profiles: BaseDeviceProfiles.ini is in the Engine folder, DefaultDeviceProfiles.ini in the Project can override settings.
So it looks, like creating a DefaultNNN.ini in Project directory for the BaseNNN.ini in Engine directory to get project specific settings seems to be the general way to get project specific changes.
BTW: see also my post here on the topic of project specific ini files - there seems to be some documentation bug for the device profiles.