No, the new behaviour is fixed. Whatever is the topmost clip gets played, which you can manipulate with the right click option "bring to front". Though if you set the clip attribute "play hidden clips" it will do just that, which can be essential if crossfading two clips on the same track.
Is your problem one of file management, in other words, the new arrangements create a lot of clips you don't want? If so, the best way to manage seems to be to use the "remove hidden clips" option, which takes all clips apart from those on top out of the session. Then use "save session as..." and tick the box which says something like "save copies of all associated files", saving the whole thing to a new folder - but not the clips you are not using. Now that's actually a good backup routine - you've now got your original folder with its full set of clips, plus the new folder with its only-current set of clips. Tomorrow, work on the version in that new folder, and at the end of the day, repeat the creation of a backup, and delete the original folder - hopefully by now you really don't need any of those unused clips. Continue in like fashion. So you will always have a backup in a different folder, and you can always go back to yesterday's takes if you suddenly realised you did want one of them.
Well the problem is not exactly file management, other than larger files. As I record, if I make a mistake in the middle, I want to pick up from that point. the problem is that the new clip doesn;t entirely hide the old clip, so as a result, the remove hidden clip option doesn't actually work. I end up with a bunch of longer clips then I need.
But I guess the method you talked about for backup helps, and truth be told I only need the final recording - the clips are no better then the final exported single audio file in this case (since they can function as the source if i need to make changes), so I can erase them without any worry at all.