Reporting here because the patch I sent on IRC seems to have gone unnoticed.
Created attachment 104118 [details, diff] Patch for the ebuild Excludes net.lo from the check for old style symlinks.
The only issue I have with this is that as of 1.13 net.lo has itself become a symlink, so this patch only applies when you upgrade from 1.12 AFAIK
This should be fixed in baselayout-1.13.0_alpha11. Re-open if you disagree.