I think the difference is that this occurred on launch day. People who pre-ordered had a reasonable assumption that anybody who bought the game on launch day would pay the same price.
If I buy something for $20 but then don't play and six month later it's on sale for $5 then that's my fault and to be expected. But if I pre-order a product for $20 and found out that others who didn't pre-order got it (or could get it) for $0.01 with MORE goodies than my $20 pre-order, on launch day, I'd definitely be upset.
Anyone who'd do a 0.01c thing is a creep! making people make a loss on the transactions.
And you still now get a lot more in the bundle than in the gog preorder, since the art and soundtrack are also in. And I agree it was crummy of the devs to do that, i suspect gog.com might not do preorders of new indie stuff again in a hurry.
Pricewise though it does happen quite regularly when you preorder - not to the bundle extreme like this but it does happen that another site does a better deal at or before launch than the one you paid. Or within the week. On indie stuff, Steam is often behind, launching a week or two later, but for less.
That's why I never preorder anything mainstream or indie unless I want to specifically support the site or the dev - then even if it happens that Steam launches it 2 weeks later at 50% of the price, I dont feel cheated. Which is what I thought I was doing with the botanicula thing. Well those devs won't get my money again even if they do the best game ever.
On the other hand I've got quite a few games (20+) I did preorder or buy from the dev at higher price because I wanted to support them. No regrets even if, in some cases, the game in the end didnt tick with me - or if it ends up in a bundle... I just preordered Age of Decadence and Xenonauts recently (and kickstarter for 2 other games too)... And I will preorder soldak's next game Drox Operative as soon as it is orderable, just because, I will also preorder mega-mainstream Guild Wars 2 because GW gave me so much as a game.. and if there's ever a Dominions 4 or a Creeper World 4 etc.