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You can safely remove virtualmin-base.
It only really does stuff on three occasions:
During installation, when it configures all of the relevant services for use with Virtualmin.
When we roll out a new package that we consider important enough to be on everyones system. But, on this latter count, we pretty much don't use it for this purpose any more.
When we need to make a change to everyone's configuration to correct issues or add new functionality safely. We don't use it for this anymore, really, either. These days we integrate this kind of change into the module that needs it (usually virtual-server).
So, go ahead and pop virtualmin-base out and pop in your replacement BIND. Just don't remove any of the other bits, and you should be fine.
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