You are not wrong about conceptual limitation, but any development convention is inherently about constraints. Constraints are “bad”, but they are also often good and important.
In this specific case it’s slightly soured by Settings API being especially nasty snowflake, which historically led people to reinvent this particular wheel a lot.
However, your estimate of flexibility seems very off base.
Any admin page can be uniquely identified, otherwise they wouldn’t work in first place. You should look at functions like get_current_screen() and work through admin-header.php.
Since we are talking in context of commercial themes in the end it’s your business decision. Some people would insists on following same guidelines and conventions as free themes. Some would say it doesn’t matter, as long as quality and security don’t suffer.
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