Sorry Sheson, was at work when I posted. Impatience...
I reinstalled xLODGen and regenerated object LOD once again with only FO4LODGEN Resources and a tree mod.
I used the default object lod settings, as you suggested.
Logs here
Some photo examples with explanation in the description
Like I said, this problem only occurs in indoor cells which have exterior lod showing enabled in cell data.
At first I thought maybe I messed my ini settings somehow but given the fact both vanilla lods and pregenerated lods from certain tree mods look fine I believe I'm somehow messing up when generating my own.
EDIT: Regenerated once more without FO4LODGEN Resources, the highway now isn't invisible however Mass Fusion building still is.