Arsh I don't recognize the yaml syntax where you are describing your network. Is this a descriptive format that you built in-house, or an input grammar supported by one of the community / Fabric configuration systems? (Not suggesting this is related to the issue you are encountering, but simply curious... it looks good!)
If `CORE_PEER_LOCALMSPID` is not specified in the env of the process running the `peer` binary, then it will use the value as defined in the core.yaml. The log looks like the chaincode commit is being invoked for the `NiMSP` org, not for the higher order education context that is hinted at by the CLI call above. There could be some other differences going on, but this still looks suspicious. (Short answer is: YES, the peer CLI env context is important - not all of the inputs to the peer binary are specified on the command line.)
