Do all NAS devices work off this same file system? (EXT4)
No. Most NASses are Linux based, and have a Linux filesystem. When looking at relative recent boxes I have seen ext3, ext4, btrfs and xfs for data filesystem. In most cases this filesystems are embedded in a Linux software raid container.
Your box has yet another layer, the filesystem is in a LVM container on a raid array.
My biggest gripe is not being able to add the 2nd disk (old data) back into the IX2-DL and being able to rebuild the data back onto disk#1 without the device wanting to wipe the 2nd disk to create a RAID set.
I understand that's a pain. The problem is that a GUI is almost by definition limited. I mean, you have to write a a fancy picture for each possible case, which cannot be done.
Of course you can copy the data on the NAS itself, (assuming the filesystem and it's containers are intact) but not by GUI. It can be done on the commandline, and fortunately all recent Lenovo and Iomega boxes provide ssh access.