The values of $wgMetaNamespace for urwiktionary, urwikibooks and urwikiquote contain spaces that need to be underscores instead (as noted at mw:Manual:$wgMetaNamespace).
Hence the following values should be set:
'wgMetaNamespace' => [ 'urwikibooks' => 'ویکی_کتب', 'urwikiquote' => 'ویکی_اقتباس', 'urwiktionary' => 'ویکی_لغت', ]
Fixing this may also fix the bug reported at T223039. (Maybe. I'm not sure.)
I don't know if a script needs to be run after this change is made.