Hello!
Since LL is based on XFCE, unless you uninstall Thunar, Thunar will always assert itself.
I don't know what effect using Nautilus may HAVE on LL as opposed to Thunar; Valtam would probably be the expert on THAT. However, on SOME of my installs, since I prefer PCManFM, I HAVE replaced Thunar with PCManFM, with - so far - no ill effects...
73 DE N4RPS
Rob