It is tripartite ,12 (3) settlement is always better for both .It is iron clad, binding on both the parties, and no dispute on the matters covered by it for the period of settlement can be raised.
Wheres the settlement under section 12(3), before the Conciliation officer, will have a legal binding for all the employees of the organisation as mentioned in the settlement, for the period mentioned in the settlement
Both are legally correct. Which one is required to be decided, depending up on the situations / conditions and parties to the settlement.
In normal manner bipartite settlement is always good for industry and proves better cohesiveness.
The tripartite settlement comes to picture when bipartite settlement fails and matter goes to labour department for a settlement. The agreement is signed between three i.e. Employer, Union and Conciliation Officer.