Yes, if you still have control over the pin via OUTSET/OUTCLR, multiplexing is disabled. When peripherals are connected they take over the corresponding control lines.
Although there are examples where you may mistake control over the pin versus control over the pull-up. For example if you enable EIC, you still have control over the pull-up/pull-down resistor if the pin is configured as an input. Externally this can be mistaken for the control over the pin.