I would love to hear more about what it took to wrestle Bundler to do what you guys needed and any insight into how Bundler's design could have been improved to make doing this easier.
The worst of it was probably the environmental contamination that Bundler does -- you don't realize it when you're running it from the command line, but it has all sorts of little system-level side effects, from setting secret config variables to updating caches. And those side-effects change as you do different things. And they're not documented.
The result is that if you want to run Bundler (or even parts of Bundler) as part of other code, you need to be very careful to establish a strict sandbox (i.e. tmp directories and clean environment are the starting point) -- and even then, it's pretty easy to get hosed.
Just figuring that stuff out took the better part of a few days, not counting the time it took to figure out how it actually works, of course.