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Very safe, I do it all the time. It is especially safe if you handle the combat movement yourself, moving away from fire, burning arrows, clouds of gas, etc. Watch the targeting, however. If you're not careful you can end up pulling something and having the entire raid yell at you. You can adjust targeting in the bot and/or class config, depending on the combat routine you are using. The routines will typically start attacking the boss as soon as the tank does, which is a bit quick but fine. You just don't want it to attack as soon as you target something. If you can't manage to turn off the auto attack target, keep your target on yourself or the tank instead.
There may be other behaviors in the combat routine that you don't want, for a particular fight. Again, change those in your class config and you should be fine, or be ready to stop the bot if you get yourself into trouble.