This is totally not super simple in Logic. In fact that workflow doesn't exist at all. So one thing you could do is click on your marquee selection (to split the existing region at the marquee borders), then mute the new region inside the marquee and record on another track.
Another possibility: monitoring during pre-roll seems to work when you start recording anywhere before the auto-punch area, so if you place the playhead a bit - say, a quarter note - before the marquee and make sure "Play From Marquee Selection" isn't checked (long click the play button for that) it should work as well.