Hi,
As far as I know I have never received that penalty even after taking from airports where altitude showed as 2500 ft or more. I haven't checked it again before I write but based on my previous flight, what I generally go is, the moment I get a positive rate of ascend and confident that the plane is going to be airborne, I will immediately take up the gear.
Its kind of a habit that the gear comes in immediately on take off. For this, get to the spot view once you reach Vr. (Speed Rotate). You can have a good look at the plane lifting up and immediately press the G key. This also helps to reduce the drag and help in the faster climb (reduced drag).
Hope this helps.