Is there a reason you can't just add them to $wgExtraNamespaces? As long as the wikis are known (meta, testwiki, etc), then you can just apply the namespaces to those wikis.
This is what I'm doing. It just happens in the setup script, CentralNotice.php. Ideally I would gate the addition of the namespaces on if the user set the option to use the translate extension.
If you're suggesting that I just add them to wmf-config/CommonSettings.php as a manual step for those particular wikis in our cluster; I'd rather not -- the namespaces are something that CentralNotice + translate requires, so I feel should properly reside in the extension config, not the site config.
That being said; if there is no programmatic way to add namespaces post init, I'll do it the hacky way. I just want to make sure that this is the consensus practice on how to do this.
~Matt Walker