Add an additional name field to the vendor maintenance window that represents the DBA information for vendors that need to report their 1099's this way. Then program the 1099 report to be smart enough to format the 1099's correctly depending on whether there is a value in the DBA name field or not.
I have dealt with DBA 1099 reporting a number of ways over many years for many clients (e.g. modifying the 1099 report to pull in the Address 3 or contact, or creating a conditional report that prints one thing if one address ID is detected and another thing if another is detected. There are probably many other workarounds as well, however simply adding a field to track this scenario seems to me to be a simple fix that would save a lot of people a lot of time and effort modifying their 1099 reports and/or updating their vendor addresses in ways that otherwise don't make a ton of sense.