You forgot to mention. This vibration comes with and without Auto Brake Hold and stopping on a signal with AC off and lights off D mode condition which is inherent in civics especially in Turbos all of them. I like you start feeling it after firmare upgrade made my car checked at 3S.
After a lot of research diagnosed it to be inherent as in this particular condition rpm drops to 600/650
Nothing to worry about all normal. 
Try switching ON the parking lights or AC / Climate control ON and the rpms will be raised back immediately and that minor vibration will be gone.