I don't have an answer for you. I use a Nikon D90, and I consistently get overexposed images. I have decided that is because I don't really know how to use metering properly in the camera. I have compensated somewhat for the "problem" by setting my camera to underexpose by -.7. That seems to work pretty well for me. Instead of applying the preset, you could adjust the exposure as needed on one of your newly imported images and then save new camera defaults.
I really think a lot of my overexposure problem can be attributed to not using the camera meter properly. Maybe I would get better results if I devoted some time to learn the right way. That probably isn't your problem. But I have learned how to compensate for myself.
I don't think it is from the camera. JPGs are fine and properly exposed. The embedded JPG is fine and properly exposed.
When processing the RAW data from the camera Lightroom does not read any special settings or profiles you have set there.
Also make sure you do not have "Apply auto tone adjustments." selected in your Preferences> Presets tab> Default develop settings.
Lightroom works just fine with the raw files from my OMD E-M1