There's nothing like that in the Beancount codebase. I've thought about building something to automatically insert imported transactions in the right "section" (I personally use org-mode, where each section corresponds to an institution and its related group of accounts) but it's unclear whether that would generalize.
I think you could turn this into a simple classification problem. Given some syntax for splitting up an input file into sections (e.g., some regular expression matching on a title or separator), you now have groups of transactions and inputs. Somehow reduce this to a simple model for classifying which section an incoming transaction matches with highest probability and insert it there. Or more appropriately - since transactions are imported in groups - find the section that best matches all the transactions in the imported files and insert at the end there.