I am not 100% sure if I understood correctly. But the Drupalized version that you have seen has features that A2Billing does not have. The only common thing between it and the current A2Billing is the AGI script that make the calls and 90% of the DB cause we have added more tables and modified some existing table.
The idea was to help ourself first cause we had many needs that A2Billing could not satisfy right away. One basic example for example is the need to batch delete stuff after selecting them by activating checkboxes. Another need was to have virtually unlimited theming possibilities and the modular approach and a hock system that avoid hacking into the core files.
A2Billing is getting there, but we need these things right now. I am not saying that A2Billing will use Drupal, but it will be much more powerful that it already is.
At the time we started it, it was easier and more cost efficient for us to develop from scratch than to try to first understand and then improve the framework that is currently powering A2Billing.
If there is an Upgrade in A2Billing, depeding on the new features, we may choose to port them on our Drupalized version or not. Our Drupal version is not mean to be a replica of A2Billing on Drupal or a competition of any sort. It is just what it is: Our Drupal Version of A2Billing.
Also, we are not building it thinking that we will have a central database with tons of clients. You have to understand that A2Billing is not a community based application. It is a business oriented application and as a business, I will not allow multiple clients applications to connect to the main thing. Basically, in the model we have, the same Web server will present the corporate Website, the customer interface and possibly the reseller interface. The relevant theme and connect will be automatically displayed based on the domain name. For instance:
https://clients.somedomain.com --> Customer Area
http://ourdomain --> Public/Corporate Site
http://reseller1_domain --> Reseller #1 Area
http://reseller2_domain --> Reseller #2 Area
The whole package will also include an improved Accounting capability and stuff like Discussion Forum, ...
So sum it up, it is going to reflect most of our business logic from one end to the other.
We will not worry much when new version of A2Billing will come out. In fact, our interface do not negate A2Billing's. We are still using both.
Cheers