I usually apply a transform or use a shared coordinate system. The first job where I experienced the negative effects opened my eyes as to why you want to be close to 0,0,0. The engineer had his model zero many miles away. They kept the survey coordinate location and my model file was instant bloat. Everything does math related to 0,0,0. When all your coordinates of objects have values that show like"6.0640078e+44" then that's too far.
I'd say it really depends on your purpose. In Navis, once you apply transform, it stays. If the models get updated the transform holds. My workflow is to get arch revit model into navis as my base. I then append my very minimal model for the purpose of alignment. That is when I see how far from 0,0,0 I am. If my model requires sharing with 3rd parties for BIM coordination then I will move my model around so BIM coordinator doesn't complain. They don't want to deal with applying transform to every trade.
If any Navis work is in house then I'll usually place column line intersection A/1 or whatever at 0,0,0 at el.+0'-0". If you then receive files from other trades then most times you can simply match the transform you gave the arch Revit model to align to your model.
This is only a small example of scenarios. If you add point cloud data into this mix, well, ask the provider of the data to align to either your coordinates or the Revit model. For me, I have not mastered relocating point clouds so wherever that cloud imports too is where I start.
...and fix the kiss export issues.