Why has it been necessary to make changes in the constitution by methods in addition to formal amendment?

The framers of the Constitution knew that it would have to be changed in time. The allowed for amendments so it could be updated as the world changes. They also made it difficult to amend so it would not be changed unless it was really important. There are no other methods of changing the Constitution unless you are talking about activist judges who think it is a living document and can mean whatever they want it to mean.