I honestly don't have any problem with other players while leveling my characters or using GatherBuddy. Try botting for a few hours unwatched, come back and press "E", if there weren't any whispers then you're probably fine. Unless you're an active member of a guild, which you shouldn't be on your botting toon, you'll pretty much be left alone.
I don't advise leaving BGBuddy unattended though, at least not in it's current buggy state. Nor do I advise leaving botbases that make you interact with other players (such as dungeons ect) unattended.
Anyways, as long as its something that is isolated such as gathering or questing, the only monitoring you'll need to do use bot around the same times each day so that it makes you look more human and do not bot for ridiculous periods of time per session (don't bot for 12 hours at a time).
Hope this helped.