This issue is the same as with 5.3.11-rc (EZP-26670), but for 5.4.9-rc.

After updating to 5.4.9-rc I have 5.4.8 reference both in setup wizard as in Dashboard

Steps to reproduce

-untar 5.4.0 tarball
-Follow 5.4 update unstructions
-Change your composer.json to update for rc

        "ezsystems/ezpublish-kernel": "~5.4@rc",
        "ezsystems/ezpublish-legacy": "~5.4@rc",

-do a composer update again: php -d memory_limit=-1 composer.phar update --no-dev --prefer-dist
-Start setup wizard
In the first screen, we have "Welcome to eZ Publish Platform 5.4.8"

After installation if we access admin interface and go to dashboard, we see "You are running version 5.4.8 of eZ Publish."

the packages I have are

ezsystems/ezpublish-kernel                   v5.4.9-rc1 eZ Publish API and kernel. This is the heart of eZ Publish 5.
ezsystems/ezpublish-legacy                   v5.4.9-rc1 eZ Publish LegacyStack (4.x)