It "takes it into account" in some way, but I don't think in the correct way. When we head downhill, the instant gas mileage that normally displays "99" when coasting actually drops when you go into heavy regen. I think I've had it drop all the way down to ~40s. That makes absolutely no sense. If anything the mpge under regen should be negative. Even if you assume that it displays the negative value as positive, it doesn't match what you'd get based on the kW regen from the ehybrid display and the speed.
To correctly keep track of the average MPGe it would need to keep track of whether energy consumed came from charging the battery instead of from regen, and I don't think it does that.