Luckily i found out the cause.
The property i was trying to set is phoenix.schema.isNamespaceMappingEnabled. The property had phoenix. which is a prefix for the phoenix interpreter. so it was not set properly on the interpreter side. so the right property i need to set is phoenix.phoenix.schema.isNamespaceMappingEnabled so the prefix gets correctly parsed. I found out this from the logs
JDBCInterpreter.java[open]:142) - key: phoenix, value: schema.isNamespaceMappingEnabled (before the change)
JDBCInterpreter.java[open]:142) - key: phoenix, value: phoenix.schema.isNamespaceMappingEnabled (after the change)
Hope this helps