They're generally known to profile on a per-account basis. If you're switching between botting and legit play, then you're giving two different patterns of data; giving them a red flag.
Botting one account shouldn't leave a seperate, legit account at risk. Not unless you're trading between the accounts in question, which would only result in a ban because your legit account is now in possession of illegitimate items.
All IP flagging does is say "Hey, this IP is known to have been used by a bot". This information is pretty useless, since each IP can potentially be used by hundreds/thousands of different people, and isn't generally effective for catching bots. I like to believe their detection is based primarily on behavioral analysis on a per-account basis and nothing more (beyond a small number of other mechanisms).