The only in #2 would normally be understood as applying semantically to one (“only one cup”). An interpretation where it applies to make is possible in a very contrived context: Today you will only make one cup of milkshake. You cannot drink it.
To me, the only in #2 means that, you haven't to do anything today, except for making one cup of milkshake. And #1 means, the number of cups of milkshakes that you make today, is only one.