I2C communication with different power sources
Yes it will work even there is a few voltage gap between the two regulators. However, this gap need to be smaller than 0.7V in order to prevent inner protection diode to conduct and cause (little) damage to the chip over time. Supply has to accurate to prevent this to append. Resistor with low tolerance value should be use to provide to configure the LM317 regulator. 

When startup, both µC won't be powered at the exact same time. The bus line will eventually be powered before both µC (through R1 and R2). But this shouldn't cause any damage due to the low current flow (thanks to high pull up resistor value).

Thanks to JimmyB, glen_geek and Janka who helped me in the comment.