You have stated that the neighbor has made a complaint against your unapproved construction and quoted it to be illegal since you have not obtained permission.
My question is that whether you have applied for permission form the authorities to raise the additional floor and the proposed penthouse?
If not, then apply for it and get your permission or get it rejected after which you can move court or sail along with other owners who have constructed the so called illegal constructions.
Did you receive any notice from the GHMC after the neighbor made the complaint against this?
If not wait until then and in the meantime since there is no restriction or stay, you may proceed with the constructions which is underway.
After following the legal steps, you may approach court with an injunction suit seeking to restrain GHMC from stopping the construction work in progress owing to its ineffectiveness towards other structures which have been illegally raised in the surroundings. Though this suit may not be maintainable but it may give a relief till such time while the local civic body decides to regularize such illegal structures by imposing penalties.
Consult a local lawyer on further issues.