Well the way threads works normally..... when you have not reversed the order....
If the thread has 3 pages.... when you click into a thread that has new replies.... it should go directly to that page, and jump down specifically to the first unread post.
This is normal behavior.
So your reason to reverse the threads because users don't want to scroll, never really made sense. There shouldn't be a need to scroll to read new threads.
Not sure how this behaves when you reverse the order. The system that tracks the new posts is a bit more complicated than changing one word I'm sure.
I will have to put on a fresh pair of eyes and perhaps try and see how that is working this weekend.
My gut reaction is that each post has an anchor tag in it, and maybe it's jumping to the wrong end of that list... and there may be a way to reverse that.
But without looking I'm totally guessing. Even I was amazed at how easy reversing the order was (in flat anyway).... so maybe I will be surprised by simplicity here as well.
Let's hope.