My point would be that the selection criteria isn't particularly robust/strict.  Iptunnel, df or du for example are not required to the best of my knowledge for system booting or emerges.  Dev-lang/python is on the other hand required for emerging (and is not a "sys" package).  I'm also not sure that the warnings are strict enough.  In order to upgrade a package (util-linux I think) recently I had to unmerge a library package on which it depended but which conflicted with an upgrade to said library.  The unmerge of the library package broke either fsck or mount (I can't remember which).  Had I tried to reboot before the upgrade was completed there would have been problems.

Big "red warnings" are of no use when one is doing semi-automatic-upgrades (and colored encodings are normally disabled when one dumps the emerge output to a file).  What is needed is a separate indicator in emerge outputs indicating that an upgrade is potentially "Dangerous" or should require "Manual" intervention.  Anyone who is not a full time developer but who wants to maintain a relatively up-to-date Gentoo system (which IMO is its primary advantage over "packaged" releases such as RedHat, Ubuntu, etc.) is going to want to automate the nightly emerges as much as possible such that no user intervention is required.  And that probably works 90% of the time.  But there are those 5% of emerges that fail "reasonably" and require some intervention (e.g. bug reports) and those 0.1-1% of emerges that fail (or even succeed) with potential problems that could cost the user days.  It is that final category (and it isn't every binary produced by a sys* package) that I am suggesting warrants more attention.

Robert