Thanks for taking care of it! :)

The upload directory is actually exposed to the web as (wiki1|wiki2).example.org/images. Depending on the host, one of the two source directories is aliased by Apache (e.g. Alias /images /var/www/wiki1/images)

I'm aware of 1., though these wikis have been running for almost a decade without any trouble.
I don't quite understand the second point though. Do you mean that having $wgUploadPath set to e.g. {$wgScriptPath}/images-wiki1/ and {$wgScriptPath}/images-wiki2/ respectively would help here, because the path is no longer named images/?

I observed the variable values at the end of LocalSettings.php. Would that be the correct point or is it too early?
$wgResourceBasePath and $wgScript are empty, $wgLogo is /images/logo.png (as can be deducted from the provided example config - $wgScriptPath is empty as I run the wiki at the root directory of the domain).

This is MediaWiki 1.28.0.