Hi,
Did you fix your problem? I have never had this issue. I use Premiere Pro CC version 7.0.0 (342) and it all works fine with the in and out points for me. The playhead also just jumps to the end of the inserted clips. Maybe there is an update that will fix this bug? Try the Adobe support and tell them about the bug, they like to fix problems in their software!
For the second problem I don’t know of a work around for that besides using an overwrite edit with the correct track selected. As I said the in and out points with a nested sequence works fine for me and I get the original clips, not the nested sequence.
Can’t think of anything else unless you are using wacky file types that are freaking everything out.
In summary, I cannot help you, but thought I would write something as no-one else has!
Cheers,
Harry