The lepton i2c are actually not fully upto the i2c spec. They are not purely open-collector as they should be. So any voltages above 2.8V go into lepton. The best solution would be to run the i2c with pull-ups to 2.8V only. or use some level shifting IC.
For a robust production application, I would recommend level shifters between all the lines. but for experimentation and testing of the lepton, I have found the voltage differences not to be a problem. The breakout goal is to just expose the raw lepton lepton lines to a more practical 100mil header to develop a custom application around.
The 2.8V regulators are the ultra low noise FT533GA.
and the digital core of 1.2V is the AAT1146IJS-1.2-T1. low noise is really only critical on the analog 2.8V.
Heat generated from a 1.2V LDO would cause issues with the lepton maintaining calibration. and why a 1.2V switcher is recommended. (if using a 1.2V ldo it needs to be placed far away from the lepton so heat does not go into the lepton)
One last note. the pure thermal 1 board digital core is at 3.0V and analog is 2.8V. this makes interfacing with 3.0 logic simpler. note that the max the lepton digital can run at is 3.1V so running at 3.3V is not viable.