"replace with newer versions from the archives" is not what's happening.
It seems to replace with identical versions, just from the archives.

On Wed, Feb 26, 2025 at 10:39 AM Philip Kaludercic <philipk@posteo.net>
wrote:

> Eli Zaretskii <eliz@gnu.org> writes:
>
> >> From: Ship Mints <shipmints@gmail.com>
> >> Date: Tue, 25 Feb 2025 15:35:10 -0500
> >>
> >> As part of my production upgrade to 30.1, I wrote a program to install
> >> my local ELPA tree from scratch, and take the opportunity to prune and
> >> curate packages.
> >>
> >> One thing that surprised me, that I didn't notice in 29.4, is that if
> >> 'package-install-upgrade-built-in' is non-nil, 'package-list-packages'
> >> reports built-ins needing upgrades from ELPA but to the *identical
> >> versions* in the 30.1 tree.  I was expecting upgrades to be actual
> >> upgrades, not side-grades, as they say.  The reason I didn't see
> >> this on 29.4, is that the distro versions were older than ELPA so I
> >> was happy to take the upgrades.  This does not appear to be a
> >> regression, just a general bug report.
> >
> > Philip, could you please look into this?
>
> (emacs) Package Installation says:
>
>    If you customize ‘package-install-upgrade-built-in’ to a non-‘nil’
> value, be very careful when using commands that update many packages at
> once, like ‘package-upgrade-all’ and ‘U’ in the package menu: those
> might overwrite built-in packages that you didn't intent to replace with
> newer versions from the archives.  Don't use these bulk commands if you
> want to update only a small number of built-in packages.
>
> I read this as that OPs behaviour what the option intends to do.
>