Yes, it is possible to connect to two different ROS masters simultaneously from MATLAB. These two ROS masters do not share information and must have different port numbers. Connect ROS nodes to these masters based on how you want to separate information across the network.
Create two ROS masters on different ports.
m1 = robotics.ros.Core;
m2 = robotics.ros.Core(12000);
Connect separate ROS nodes to each ROS master.
node1 = robotics.ros.Node('/test_node_1','localhost');
node2 = robotics.ros.Node('/test_node_2','localhost',12000);
Clear the ROS nodes. Shut down the ROS masters.