Sorry about not updating this thread.
The entry checkpoints and the parking is out sourced to some third party company so they redirected me to them. Their guy called me and told me to bring the car to some random shop where they get their work done from. I Insisted I won't get it repaired from anywhere other than Honda and he was like, app yakeen karain acha kam ho ga, best quality and all that. I decided to leave it as it is because most denters recommend not to get that repaired or it will seriously damage the resale of the car as it will be considered roof damaged car or something.
Guys at honda point buffed it with the machine for few seconds and it took care off all the marks. The dents are invisible unless you really look closely or car is parked under the sun or any other strong light. I have even forgotten about it.