Why does the high Side Current Shunt monitor fault as soon as power is on
Figure 1. Problems with logic levels?

I haven't looked at the INA200 datasheet at this stage but it seems to me that you have a few potential issues.

Q1's emitter is pulled up to 3.3 V at (3) and (4)but the very most its base can reach is 2.5 V at (2) even if (1) is running on 5 V logic. 

Is this intended design?