You can use round brackets, but then you would need to make use of a valid anchor name and syntax, since at that point it is a “non-magical” direct link that just so happens to point to something in the document rather than anywhere in the world. The square bracket method is designed to be a writer-friendly tool, so we can merely type in the section name naturally, as we would refer to it ourselves, rather than, [My Link Source](#my-link-source).
But it does presume the heading target is in the same context as the reference. As for breaking that (splitting files and putting things into different contexts), I feel like this specifically has already been discussed, and established that one should be using Quarto’s cross-referencing syntax for multi-file site management, rather than pure Markdown. I.e. not using Scrivener’s convenience pure Markdown converter.