It is the same thing. Since ver 17. MC supports also separated into 4 parts config file (general, wallets, algorithms, pools). It is done to make easier config replication between rigs (basically you need to correct algorithms part only, others may be copied without changes).
Usewindow can be set either globally in "general" part, in this case all miners will start in separate window, or for particular coin, applied for this coin only.