I spoke to Geoff a while ago about this and at the time I was dubious as well. However, the more thought I've given it, the more it makes sense to have a separate package manager for browser apps. The problem space is fundamentally different that that of npm. With the browser, you PM is inextricably linked to your build system. NPM was never designed with build considerations in mind.
Apparently they have their own reasons[1] but most of these are questionable. As I see it, this is just lock-in, NIH syndrome or just bad engineering.
[1] https://github.com/meteor/meteor/pull/516#issuecomment-12919...