There are many clever ways to stack subs, like you mention, ZWO is doing none of that. They accept/reject subs based on reasons like "star trails" or "not enough stars in image" - and they reject an amazingly high number of them, between 20% and 40%, and then they just accumulate the "good" subs, including those with satellite or airplane trails. Of course, it would be much better to accumulate pixels selectively, instead of on all or nothing sub base, especially when you do mosaics and more advanced processing.
Right now we have to live with these trails and luck, if they happen early on during the capture they get averaged out, if they occur toward the end, you are stuck with them.