1) I don't understand why there is a difference - when it is exactly the same command.
The load command loads the data into the caller's workspace. If the caller is the command window, the data will be loaded into the base workspace. If the caller is a function, the data will be loaded into the function's workspace.
2) Is there a way of just adding the 'ZaphodBeeblebrox' part to the Base workspace (when doing this from Appdesigner) and loading from a MAT file ?
You can load specific variables using this syntax: load(filename,variables) but I recommend using the output syntax in addition to that S = load(___).
You're requesting to load data into the base workspace from app designer but then the data wouldn't be accessible in App Designer without using risky methods. Instead, load the variables within the callback function and store them directly in your app.
The callback function would look something like this after you declare FileData as a property (see link above).
% Load the variables into a structure.
S = load(filename, {'Var1', 'Var2'});
app.FileData = S;
Then you can retreive the data anywhere in your app by using
app.FileData.Var1
