Floating Differential measurement?
Ok, came here to post what I was missing and found that Finbarr already mentioned this in the first post's comment as well:


  "How does a multimeter achieve differential measurement?" It doesn't
  have to. It uses the common input as ground and measures the voltage
  at the other one. – Finbarr


Yes, so I didn't set my reference right.

As long as I reference my opamp's one input to the floating GND I can measure directly what the other input sees. So differential for the otherf loating system as long as I put my opamps GND in the correct place.

I built this circuit. Non-inverting amplifier with gain of ~10x
Simulated with some dummy loads and it seems to measure small voltage drops very nicely. Just enough for my purpose.


There I measure across R2 so that non-inverting is on the high side and the non-inverting input - which is actually my measurement-circuit's ground is on the low side of the 'DUT' - thus it makes sense in simulation as well.

In my use case I won't worry about the common-mode voltage range. The inputs location is fixed (such as in the simulation) and the voltage between the op-amp inputs cannot exceed +-6V there. So I should be fine.

Added an extra buffer stage in the end so that the ADC wouldn't load the first stage's feedback circuit. This might not be a problem, but I added it just in case, since I had a spare opamp in the package.