I think jacksmack's point is that there is no option available to just say "Do not limit me by the sets I have". (Maybe that would be a 'set' you could click, that would change all card quantities to six?) This is an option I would like as well, and until it is available, I will not be using this builder. Don't get me wrong, it looks rather useful. But the unnecessary, programmed-in limitation turns me off as well.
1) As already pointed out, limiting by sets is pointless when the program cannot accommodate already-created decks.
2) What if we have promos that have since be released (Galador, Meditation Amulet), and so extra 'valid' copies of a card beyond what the sets alone would account for?
3) This is supposed to be a book-building tool. My personal method of doing that is to include every card I would *like* to have in the book, and then start choosing which ones to remove until I reach 120 points. I don't consider this a good tool to support that build style.
4) Why are we inherently limited by set quantities in the first place? Again, I understand many players like to build based on the cards they have, that is not my question. My question is, why is there not an option (such as setting every card quantity to six) for the players that don't want to be limited that way?