1. The white and blacklists affect the query interface, which is instance wide, so in that way yes it affects all virtual servers in that instance.
2. One of the issues that arise from that is that you can do whatever permissions allow you on any of these servers (which you can already), the difference is that now, you get kicked / banned if you overdo it ie. spam commands. With the IP whitelisted you won't have that limitation which might concern them. You still shouldn't be able to do anything too bad but better safe than sorry.
3. Each hoster has its own policies.
4. Make sure to not send too many commands to the query in a too short amount of time.
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