For your first question, you've specified the format that datetime should use to interpret the representation of the time that you passed in, but you didn't specify the format in which the created datetime should be displayed. To do that, specify the 'Format' name-value pair argument (just like you specified 'InputFormat', with the desired format as the value in that pair.
dt1 = datetime('now')
dt2 = datetime('now', 'Format', 'yyyy-MM-dd HH:mm:ss')
For your second question, if you've previously plotted a line whose x data is numeric, you can't add another line to that same axes whose x data is a datetime.
x = 0:360;
y = sind(x);
x2 = datetime('today') + days(x);
For this particular case, there's a reasonably intuitive mapping between x and x2. But in general there wouldn't be. In those cases answering a question like "Does x = 28 correspond to a week from now?" to line up the two plots could be difficult.