In one sense you're right. There is a historical relation. However, I'd argue that that relation is so obscure these days that no native speaker would even thin

In one sense you're right. There is a historical relation. However, I'd argue that that relation is so obscure these days that no native speaker would even think about it, unless it's pointed out of course. But yes, the origin of the letters is indeed from their base, where ä came from an e written on top of the a. This is more clear in Norwegian where you write the same letter like this æ. These days, very few people (outside of liguists working with the history of the language) would argue that ä is a variant of a though.