If I am long on a scrip (e.g.) Nifty futures in an MIS order, and another intraday strategy requires me to go short on the same scrip, can I go short with say e.g. BO? Would these positions cancel each other out?
You can do it. Both the Positions will show you separately.
MIS and BO are intraday products and these two are totally different , so you can place these orders and system interprets these orders separately.