Excessive Ground-Loop/Discontinuity?
No, this will not cause a problem. The high-level input voltage to U3 will be about 0.1V below the power supply voltage of U3. That input voltage is still well within the voltage range that will be recognized as a logic '1' by U3, and the slightly lower voltage will not damage U3.

The only possible disadvantage to this arrangement is that the power supply current drawn by U3 will be slightly higher than it would be if the high-level input came all of the way up to 5.2V. I doubt that you will even notice this if your board normally draws 2A.