I just had two D800's converted - one to full spectrum and the other to 720nm. The idea of the on-sensor 720nm conversion was so I could do some hand-held shooting as well as use use lenses like the 14-24 without worrying about filters. Again, the plan was to use the OVF and AF. I also have a Coastal Optics 60mm which is likely the only lens out there without any focus shift across the full-spectrum. So the flexibility of using the OVF sounded very good.
The full-spectrum would always be used with on-lens filters and the plan was to use LV focussing.
Now that I have tried the setup with both bodies for a couple of days, I can confidently say, at least for the setup that I have, composing/metering/focussing on the sensor with LV is the only way to go. WB, focus, and Exposure are all different with a mirror vs. right on the sensor.
AF and MF with the mirror is so off that it is off the scales of the focus tuning scale of the D800.
So if converting an MFDB, I would ensure that either LV is available on the back and "usable for you" or you will be shooting tethered.
Just my 2 cents. I know Graham has a D800 converted to full spectrum by the same company, and you want to get his thoughts as well.