Update
Thanks to a 3rd party plugin, SlowCheetah, this is now possible. Scot Hanselman has a blog post about it.
Original response:
Unfortunately, the web.config transformations appear to effect only publishing sites and building deployment packages.
In our scenario we have two development groups, one with access to multiple environments (in-house) and the other with access to a single environment (offshore). We have periods where the in-house group needs to debug directly against QA, while offshore remains locked-out (so their web.config's must point to the dev environment).
We were hoping to have 1x build-configuration per-environment, and be able to choose the build-configuration which matched the environment to debug against--which, as I understand it is your question.
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