OK, you asked for an easy way. Depending on how you look at the following, it maybe easy or not :)
It looks like sim itself does not allow for the 2 approaches to be combined. So the way to do this is to use configuration parameters set specific functions such as getActiveConfigSet and setActiveConfigSet. Following is an example function to show how to do this:
function runFooModel(mdl_name)
% Input mdl_name is a string
%Get current config set of the model
configSet = getActiveConfigSet(mdl_name);
% Create a copy of the set to manipulate it. Alternatively load one
% from an existing file
configSetCopy = copy(configSet);
% Make a change. Again, if this is another config set, this step is not
% necessary since the object will have the change built in
configSetCopy.set_param('StopTime','50');
% Set the new config set as active
setActiveConfigSet(mdl_name,configSetCopy)
% Sim with the new config set
sim(mdl_name,'SrcWorkspace','current');
% Optionally revert back to the original model config set to
% restore status
setActiveConfigSet(mdl_name,configSet)
end
Also note that based on the documentation for sim, The sim command accepts all simulation parameters as name-value pair arguments. See Model Parameters for a list of all simulation parameters. In addition, the sim command accepts a list of parameters that is sim command specific. However it looks like sim does not allow for the 2 approaches to be combined. Some of these parameters could be in the configuration parameters set so we could work around that way and call sim with only the necessary configuration parameter set. However unfortunately, SrcWorkspace doesn't seem to be a parameter in the configuration parameter set. So the way described above seems to be the workaround.
