Storing values in the ROOTs ApplicationData or UserData is valid - as long as you do not make any mistakes. Sharing a single object is equivalent to using a GLOBAL variable. As long as you care for correct writing, especially by using a unique name for the variables, everything wents fine.
But is any problems occur, debugging will be much harder. An additional data handling layer can be very helpful then: Create a function, which is responsible for all read and writre operations to these data:
function Data = DataHandler(Command, Data)
switch Command
case 'put'
setappdata(0, 'DataHandler', Data);
case 'get'
Data = getappdata(0, 'DataHandler');
otherwise
error(...)
end
Then setting a single breakpoint inside this function let you observe any change of the "global" variable.
