The following will unpack and apply patches, but it won't run the configure script:
ebuild `equery which app-shells/bash-4.2_p10` configure
To run the configure script, I need to tell ebuild to compile bash, rather than to configure bash. These should be separate stages.
The ebuild has EAPI=1 so src_configure is not a valid build phase and is ignored, which is fine. The problem you are looking at is that ebuild(1) should probably fail when an invalid phase is called.
ebuild does abort for generally invalid phases (try "ebuild ... foo"), but it silently skips invalid ones based on the active EAPI