Something is not right then, you shouldn't see idle speed increase when you take the car out of neutral in a manual.
My Black U12 has never done it, my TRX has never done it. The other TRX I stripped didn't do it either. No other manual equipped car from other manufacturers i have ever driven have done so either.
Checking yesterday, both in and out of gear, my TRX idles at a rock solid 860-890rpm.
My Black U12 only had idle speed DECREASE when I put the car in gear when I used to run a modified auto ecu program, it did this because there was a table in the the program that would retard timing when it was told that the car was no longer in neutral / park. (this table is there in auto's to reduce torque output at idle, 1) so the car doesn't start driving off with the throttle closed when put in drive and no brakes applied, 2) when the brakes are applied, reduce the amount of work the torque convertor has to do to avoid unnecessary heating of the tranny fluid. This timing is generally dialled back in when throttle position is around 5-10%)
When I updated that piece of software which was then based on a manual trans ecu, no in or out of gear idle speed decreases / increases occurred.
It very well could have been a "feature" added in later models, I just find it strange since increasing idle speed that high when in gear will only increase fuel consumption when stopped at a set of lights.