I think that normally when someone says not to use the same print in a different color is when there are only 5 - 6 fabrics in a quilt. I believe that it is quite common when using a large number of fabrics such as a FQ pack, you are going to get the same print in several different colorways.
And it is your quilt, so whatever you like goes - but yes if I have a FQ pack I am using all of the fabrics in it.