I believe that the Simulink message type selection drop-down should use the same functionality as rosmsg("list"). I'm not sure why it would show different results. Did you restart MATLAB after generating the custom messages?
As a possible workaround for now, if you create a MATLAB publisher or subscriber using that message, can you use "Select from the network" to pick the right topic and message type? As another workaround, you should be able to use set_param on the blank message and publisher/subscriber blocks to change the message type to the desired custom message.