There are no problems with BIND. It all works perfectly.
We have purposefully made the ISPconfig server (BIND) unavailable publicly; it's available only to the slaves. That is not the problem.
Furthermore, I know I can edit the pri.domain.master file in the manner you describe. I have been doing it for quite a while now.
The problem is that I have to edit the file _every_time_I_upgrade_ISPconfig_. Then I have to regenerate each zone file as well, which is a tedious process with a large number of domains (I usually just change the TTL and click save on each domain). After an ISPconfig upgrade (I have done several now), the pri.domain.master file is overwritten and _all_ of the zone files are regenerated incorrectly (depending on your perspective).
Again, I realize this feature request may not affect the majority of users, but if it is easy to implement, I ask you to consider it. That's all.