Unfortunately, size does matter a great deal now. First Class has more than one charge. Basically there is First Class Flat (envelope/letters) and First Class Parcel, which is anything that is 3/4 inch thick. OR envelopes that are not consistent in thickness or shape.
I am like you. We do not know the box until we build it either. But we are going to use the dimensions anyway. We are measuring the size of the item and adding x inches on each dimension for packaging and the box.
Just so you will know, eBay's calculator has a bug in it right now. As of this morning, it is still not corrected. First Class is not showing up if you use the dimension field. And dimension is the only way the calculator can tell the difference between a letter or a first class parcel.
The First Class parcel issue isn't that difficult though. FCP is $1.13 for the first ounce and .17 for every ounce after up to the 13 ounce ceiling. There is an additional .17 surcharge for non-machinable parcels. So it is relatively easy to figure out. Now if eBay will just fix the calculator.