Methods and systems for a networked computing system are provided. One method includes generating a first proxy endpoint by a non-transparent bridge (NTB) of a first pluggable compute module and a second proxy endpoint at a second pluggable module having a second NTB, based on a user defined topology; establishing a transaction layer packet (TLP) tunnel between the first proxy endpoint and the second proxy endpoint for peer to peer communication using a first stub endpoint of the first NTB and a second stub endpoint of the second NTB; and de-allocating the first proxy endpoint and the second proxy endpoint, when the topology is deactivated such that the first pluggable compute module and the second pluggable module are available for another user defined topology.