The difference is that Afrikaans was at one point legitimately written in Arabic script: w:Arabic Afrikaans. From Wiktionary's point of view it's a dead language, really, so it kind of qualifies for LDL because there is so little of it. But it's definitely more than just "oh let's write it in Arabic for the fun of it". The Afrikaans Wiktionary itself also includes it in its entries.
Thanks for the link. Might still be easier to call it a separate L2, because a Serbo-Croatian-esque solution will look stupid here, giving way too much precedence to a basically extinct sublect.
That's why there were separate categories for it, but you deleted them. I would compare it more to Old Church Slavonic in Glagolitic. It was never as common as Cyrillic (except in Croatia) and most textbooks on OCS consider only the Cyrillic variety. But we still consider them one language.