The WHS bug was fixed in their PowerPack 1 last summer. The drives themselves use regular NTFS and the duplication mechanism just copies the files to the duplication drives so that each drive and file is fully readable by another PC. If your server fails and wont boot, just pull the drive and plug it into another machine (PC/Linux/Mac can all read NTFS) to read the files off.

Do devices like the QNap not let you do a full server backup to a USB drive in a regular format (like ext2fs)?

The biggest mistake people make with RAID1/5/6 is thinking it is a backup, but it's about redundancy. If you delete or modify a file on the RAID, then it is changed/gone just like a regular disc. However if one of the drives dies, you can just replace it and let the array rebuild. You must have a real backup strategy inplace if you want actual backup. That's why I use the WHS server backup to backup my server to an external USB drive (and also backup photos nightly to Amazon/Jungle). Backups for our computers live on the server.

Living room: DSP5000.3
WFH Office: M33
Bedroom: P200ZQ