Do you mean you want to produce a function-call signal to use with a Function-Call Subsystem? If yes, I don't think this is possible with an (Embedded) MATLAB Function block at all. Have you been able to do this manually (let alone from the command prompt)?
EDIT
Turns out, it is possible to generate function-calls from a MATLAB Function block. After playing with the Stateflow API, I was able to come up with this:
S=sfroot;
B = S.find('Name','MATLAB Function','-isa','Stateflow.EMChart');
fc = Stateflow.FunctionCall(B); % add a function call output to block
Caveat: This is not documented, so there is no guarantee that it will work in future releases.
