It is comparable to the "Multiple Applications License" provided by WrapBootstrap. Still relatively expensive since most Multiple Applications Licenses are under $99.
If this is officially supported by the Bootstrap project - this to me feels like a nuts deal.
(Same in mobile apps. $5 is a steal for a decent app/game, by any direct measure of value. But comparatively, $5 is way more than most apps.)
Here's your problem: you assume it's "the same thing". Just because the $4 thing looks OK doesn't mean it has the same code quality underneath, or that it wasn't stolen (as lots of "premium themes" are).
I've bought themes, both Bootstrap and others, that looked great, were dead cheap, and never got past the first open of the templates in Sublime Text. They were just too much of a disaster to work with.
Knowing that I'm getting top-notch quality is worth the $99 for me, if the themes fit what I'm trying to do. The amount of time saved not undoing someone else's mess is worth much more than $99.
That's not to say a cheaper theme isn't going to be good. I've also bought many that were quite good. I guess the difference here is that you can really trust what you're getting, and not have to rely on user reviews. I believe the Bootstrap people have earned enough trust where I know I'm getting a theme I can easily work with.
This feels (even in alpha) like a HUGE move in the right direction.