As a nice memory of the redhat era, I have alias rm="rm -i" alias cp="cp -i" alias mv="mv -i" when I am rooting. This means that it so happens that sometimes I leave my PC to do some emerge-ing and when I get back I see that it is waiting for me to respond to `overwite "./configure" ? ' or similar. I suggest emerge does an "unalias -a" before proceeding with the ebuild made by the developer.
Fixed in >=2.0.46-r4