Unfortunately Portage and Pkgcore have broken EAPI 2 implementations.
So far as I can see:

Portage:

* doesn't implement the 'default' function correctly for src_prepare.

Pkgcore:

* doesn't implement src_prepare
* doesn't have a working default
* default_src_configure and default_src_prepare are the only
default_s that work

Unfortunately, neither appears to have comprehensive unit tests
covering all new EAPI 2 functionality, so these got through into
package managers that made it into the tree.

This is a bit of a mess. Possible solutions are:

* Ignore it, and tell anyone using broken package managers to upgrade,
and deal with the resulting mess.

* Create a new EAPI 3 which is identical to EAPI 2. Make really really
sure Portage and Pkgcore implement it correctly before they go into the
tree. Deprecate EAPI 2, and convert everything using it to EAPI 3.

* Avoid using any broken feature, and retroactively remove the
definitions from EAPI 2. Unfortunately, this probably isn't viable
because of the src_prepare thing in Pkgcore (were it merely an
unusable 'default' we could get away with this).

None of these are very nice. Better options would be encouraged... We
have to do *something*, though, because this is hitting users already
(see bug 240684 for one).

-- 
Ciaran McCreesh