Now that core MediaWiki supports its own custom collation for the Bashkir language (see T162823), to actually make it work on a project, $wgCategoryCollation must be set in the site configuration.

It would make more sense if simply setting $wgLanguageCode = 'ba'; would also automatically set $wgCategoryCollation = 'uppercase-ba';, unless the local settings override it. This default should probably be somewhere in MessagesBa.php (or whatever the code is).