Arun at I.B.I.S. pointed to this surprisingly old and surprising useful article on auto applying AR via SQL. Essentially it looks like the transactions to apply are added to a temp table in SQL and then the SQL routine goes through the temp table and applies the payments.
This give you a a 4th option for auto applying AR (Interface, Integration Manager, eConnect, SQL) before you have to go to custom programming. I haven’t tried this yet so all the usual use at your own risk caveats apply. If someone plays with it let me know how it works.
Note: SQL Code is included in the article.