When one undergoes samashrayanam under Munitraya tradition and performs bharanyasam under Sri Matam tradition, which tradition that one must follow to celebrate festivals such as Sri Jayanthi, Karthikai Deepam, etc.?

Svami Desikan has mentioned that the Acharyan under whom one has undergone mantropadesam is the primary Acharyan. There is also a tradition that does weddings, etc. based on the lineage under which samashrayanam was done.
So, it would be appropriate to follow the Munitraya tradition under which you have performed the samashrayanam. It does not mean following otherwise is wrong. It can be said that only to inculcate a discipline that it is said one must adhere to a tradition.