I am not exactly sure what you are asking when you say, "capture that outside of Drop Multiples option". If the data table created contains all of the data you want to count, you can easily get the count with:
dtjoin = dt << Join(..............);
number of matches = N Rows(dtjoin);
Or you can also use the "Match Flag" option from the input dialog screen to create a column called Match Flag, which will have the values of 1,2 or 3. If the data is from the first data table, and no match in the second table, the value of Match Flag is 1. Coming from the second table and no match with the first table, the value is 2, and if it finds a match, it's value is a 3.
Jim