As you are using LMDE, the ISO will have installed both Cinnamon and MATE. Cinnamon is running on top of Gnome 3 (as a replacement for Gnome Shell), while MATE is a fork of Gnome 2. To facilitate MATE being able to live on the same system as Gnome 3, as well as probably some Gnome trademark removals, all packages and applications forked from Gnome 2 to MATE have a new name.
In short, yes engrampa is the fork of Gnome 2's file-roller. And you have that installed alongside Gnome 3's file-roller that comes with Cinnamon.
On the next update of the LMDE ISOs, MATE and Cinnamon will be on separate ISOs so this won't be there. The benefit of having both MATE and Cinnamon is that if the one breaks, you may be able to just log in to the other (from the log in screen you can pick which desktop environment to run for this session) and repair whatever is wrong.
As to the "extract all archives" question, I don't think this is a limitation of the archive manager but of the file manager not offering you this choice. You may try a different file manager instead.