So, imagine the scenario where you've got a commonly-used function that gets vendored and from there copypasta'd into a lib/common or some other location in your project. You've basically just cut yourself off from any updates that the module author might make when new javascript optimization hacks come around (or obscure corner-case bugs need protecting against). It's a small problem, but it is at least worth considering.
There's also this whole thing with licenses - there's a fundamental difference between using a library and copying its source into your build tree. The MIT license doesn't care, but the LGPL certainly does.
I do like the idea in general. You should extend it by doing tree-shaking or dead-code analysis. "This library is big, but you're just using one function call, let's just copypasta that one in here".