Not a developer so I'm not sure. But, 99% of what people do from the CLI, if it's anymore more than looking at things(ie checking SMART status, time check, permissions, etc.) it's something that can go badly without warning. Generally, if the manual doesn't tell you to do it you probably shouldn't. The WebGUI does things and expect nothing to be done behind it's back. If you start doing things behind it's back it'll get upset. It's caused tons of problems for people.
When give a choice between FreeNAS trashing your jail(s) and just not doing this from the CLI, guess what the conservative choice is? ;)
This is partly why the FreeNAS API was created. Too many people wanted to do things behind the WebGUI's back and it ended badly. We've had lost pools from bad CLI choices before. You should be using the WebGUI or the API ONLY unless you are 100% sure what you are doing is safe. Even innocuous things have proven fatal to configurations in the past. So don't be fooled because it seems pretty minor to do something from the CLI.