And in practice all amendments are proposed by Congress, and Congress always knows what amendments are already pending, and should be able to foresee any potential "merge conflicts" and address them. You can always use conditional patch instructions: "Replace section A with B; however, if amendment C has entered into force before this amendment, instead replace section A with D". There are other tricks too, like one proposed amendment inserts section 29A and the next inserts section 29B, and maybe if the first one never gets ratified but the second one does you end up with a section 29B without there ever being a section 29A.
(Technically there is a process where a convention proposes amendments independently of Congress – https://en.wikipedia.org/wiki/Convention_to_propose_amendmen... – but it has never been used, and who knows if it ever will be. Anyway, the same point applies to such a convention – it knows what amendments are already pending so it can write its proposed amendments to include solutions to any merge conflicts)
I think the real explanation – the US constitution is really old, a late 18th century document, before a lot of the contemporary English-language culture around maintaining legislation had developed. And now it is the way it is, and nobody wants to change it. But if they started again tomorrow it is unlikely they'd organise the amendments in the same way. And a lot of US state constitutions are newer, and they are maintained in the more usual manner precisely because they were adopted after the usual manner was invented.