I personally support this system, largely because it stops pretending electrum is really a reward (since it's so easy to obtain from the game's AI and arena) and instead offers more opportunities for players who can't get to first because there might be one person better than them. It rewards people who get second, for example, consistently, which the current system doesn't do because people who get second only get a measly 5,000 electrum with out current system. And I must say, I'm still waiting on my 3,000 from last week's tournament.
If you get second consistently you do something wrong. In fact you should not make more than 50% more second places than first places. It equals a 40% win rate in the finals. If you 'consistently' fail to do so it indicates that your decks aren't good enough and you should not win. I very much include building the strongest possible deck, winning against most decks and having to face a counter in the finals and failing to adapt.
Electrum is useless, though. Let us trade 100k worth of electrum codes for a nymph!
Addressing Sub's questions:
Two wins is too few. That's why double elimination was introduced in the first place. Of course, you can have a discussion about it but most people seem to can get behind the idea and I don't see the need to set a precedent. I like to point out again that 8+-man tournaments should reward the winner with a mark code.For fewer attendees double elimination ensured the winner had to play at least a third match.
Concerning the second question, generally yes, but starting with unbalanced bracket, say 6 players, unfairly (imo) favours some players over others. So, no. A bye should not count as a win an winning 2 matches in a 7-player single elimination does not merit a mark code.
Alternatively establish round robin for up to 6 players. Or just listen to JCJ.