If a font does indeed provide for African languages, then I think it does makes sense to have the capital “nj” form as the default, and localize for the relevant Sami languages.
But to adequately cover African languages, one needs several less common characters — such as ɓɗɖɲƴ, just to show a few.
Extended Latin character sets that cover the majority of European languages will easily cover
three of the four Latin-using Sami languages with the simple inclusion of ŋ. If the char set is primarily aimed at that standard target, then I think it makes sense to have the “NJ” form as the default.
If you want to provide a capital “nj” form for those few African languages that can get by with just the ŋ and not the rest of the pan-African set, I would be more inclined to make it the alternate.
but still if it can't begin a word, distinguishability between the upper- and lower- case forms is somewhat less of a priority.
I don’t know why on earth you jumped to that conclusion!?
Here are just a handful of words starting with һ taken randomly from the front page of the Башҡорт wikipedia site: һаулыҡ һаҡлау һәләте һәр һәм һуңғы һуғыштың — including the very common һәр “every” and һәм “and.”