Amit,
The agreement between the builder/developer and landlord is in respect of development of the property in the form of apartments/flats. In such a case, the land shall be developed by the builder/developer in the form of building and the same shall be sold by the developer/builder and the agreement of sale of the flat/apartment shall be a tripartite agreement executed between the buyer, land lord and builder and in accordance to the same sale-deed/ deed of conveyance shall be executed after completion of the sale transaction in respect of the property. The sale-deed shall be of the flat/apartment which you will buy along with undivided share in land.
There is no harm in it at all and you can proceed for buying the same. Kindly verify the documents in respect of title verification of the property on which the building is being constructed. There should not be any charge/lien/encumberance on the same prior to agreement between the builder and landlord.
In case of any further query feel free to ask.