There is no problem as such but instead you may choose some one other than builder to avoid influences.

1. A Federation of Societies can be formed PROVIDED a minimum of FIVE CHS join in as members of Federation.

2. However an Association of Societies can be formed by 3 CHS.

3. Federation /Association can be formed /registered "ONLY" by "existing" Societies and not by Builder /Developer.

Once co operative society formed. Builder will have no say and only elected committee will look after the affairs of society. No promoter permitted in cooperative society. Either there will be 3 CHS with 3 independent committees. OR 3 project under one CHS.

apex body has to be formed of 3 cooperative societies  to manage the common facilities – like Clubhouse, Common Roads, Main Gate security etc

object of apex society is to promote the principal objects of the societies affilated to it as members and to provide for the facilities and services to them,

Housing Federation is a statutory body, formed for taluka, Corporation Area or District level, by the CHSs from that area. It is formed to redress any dispute between the members of the CHS and its management.

Regarding the formation of Federation, any five societies in your layout pass a resolution to form the federation, elect the chief promoter and submit the proposal of registration of federation to the Deputy registrar of your ward.The provision of Federation of Societies has been made in the Maharashtra Co-operative Society Act 1960 and Rule 1961.

With unlimited increase of the housing societies, the problems/disputes in it have also been increased. And the complaint application had been received to the co-operation department for solution of such complaints. Limited human force of the co-operation department is very inadequate for this. The District Federation of the Housing Societies can solve many problems of these.

yes it can be formed but its not feasible to include builder as chief promoter

1. There are no drawbacks of formation of federation of societies you can go ahead with registration of parent federation.

2. But only societies can form the federation ans not builder or developer as they are not part of the societies. 

Each and every society must be formed separately. If you are forming 3 societies and a parent federation then make sure that all are represented in that federation equally. Moreover other contingencies which may arise must also be addressed.