Yeah the wallet has 100 addresses ready in its queue - most casual users are not going to use more than this (especially for a crucial savings wallet - it'll probably only have a few addresses used), and I'm quite sure the deterministic wallets will become standard, so the potential problem of which you speak should go away on its own. I was trying to make the article somewhat future-proof (and had to keep it simple), so I didn't delve into nuances like this.
100 transactions ever isn't that unlikely. And probably by the time they are putting serious money in and then retrieving their backup they'll be past that. It is sends (new change address) and newly generated payment addresses (used or not, click that button 100 times and your backup won't work from that point).
Maybe devs could change the default to 1000 if bulk generation can/is done smoothly now. But that's still not foolproof.
Yeah, 1000 isn't that big of a deal, and really 10000 isn't either (as far as storage). This extra bit of data will make it so backups for 99.99% of people would be unneeded, which is awesome.