Since the portage autoresume point is put at /tmp/.clst_portage inside the chroot, it isn't removed as part of the normal autoresume cleanup code. I'm attaching a small patch that should take care of this special case.
Created attachment 109898 [details, diff] patch to clear portage autoresume point
Alternatively, we can just kill the autoresume check for portage like you've done for ccache and distcc, since it takes very little time to emerge portage. That's probably the better solution. That will allow the patch in bug 166426 to be used with pre-existing stage3 seeds.
Created attachment 109903 [details, diff] patch to remove check for autoresume point in setup_portage()
I've gone w/ approach #2
This is fixed in 2.0.3 which should be hitting the tree shortly.