The act of the pent house owner of encroaching the terrace is illegal because all the flat owners have undivided and common interest over the said space. \
The roof is a common space and hence its use can not be restricted either by the owner of penthouse or the builder.
Firstly you confirm that if the penthouse is part of the approved plan.
If the pent house is not part of building plan, then the pent house is illegal.
If any other member of the apartment file a petition against the builder and the pent house with Municipal authorities and get the pent house demolished as illegal construction, then you will be under great trouble and heavy loss.
Also if any other owner file a petition in the civil court for injunction against the pent house owner and the builder and claim ownership of the terrace rights, then it will be under unnecessary litigation.
Therefore it is suggested that you better continue to enjoy the terrace belonging to you alone and not disturb the common terrace at the risk of losing plenty of your own issues.
You may maintain cordiality with the association and other members so that nobody will try to disturb your enjoyment of your property.
If you want to tackle it legally, then you may have to be perfectly alright in legal aspects with regard to all the issues involved in your property.