Yeah, when I found out about this it was the one inelegant thing about the 3.10 OS, I'm not sure if the 60 did this before, I think soft thru being off is supposed to disable it but it doesn't. It's a bug I think. The way I work around it is to use a track per pass. So if I play out something and it loops, I change it to midi and go to the next track to add more. It is a bit of a Kludge, but it is the only way to avoid it, but what do you care, you have 99 tracks to burn. You could always copy the multiple tracks to one track and delete the others when you are done if you want all those on one track for arrangement purposes, But I haven't found the need to do that. You learn what's where pretty quick, and my tracks rarely go over 30.
if you think that's annoying, in the same set up try using note repeat on an external unit whith local off and the track set to drum, it doesn't even wait for it to loop, the internal drum sounds note repeat too!! Again, it is all solved by the midi controller and the track switch trick eases the pain
I will try to find out more about it. On such an elegant machine, it sticks out like a sore thumb, but I usually use a midi controller and everything works as expected there.