Yeah, the qualification issue wouldn't be that bad; as it is, usually a few decent European sides stay home each cycle (this time around, that's Denmark, the Czechs, and one of Sweden/Portugal). This proposal simply moves the final round of qualifying to a global scope, so if you're good enough, you progress. It probably even helps better-than-average Euro teams. Imagine you're Denmark or the Czechs this time around. ELO has them both ranked in the mid-20s in the world, which sounds fair to me. To qualify out of Europe, they needed to finish top (or a strong second) in a group that included each other, plus Italy, plus some feisty Eastern European teams. Under the 64/global system, either would likely be in a 4-team group with one better side (an Argentina, maybe) and two worse top 70-ish sides (let's say, Senegal and Uzbekistan). A top-2 finish there gets them through. In general, better teams (regardless of confederation) are given a fairer shot than they have now.
The one flaw I can think of is simultaneous starts to end the groups, on a global scale - depending on the teams involved, the logistics could have games kicking off at crazy/nonsensical hours.