Good news. Replicated what happened in our lab, and the Smart Array didn't even blink. Here is what I did:

1. Ran around the entire lab for a while just trying to find an NT4 box still working
2. Found a Proliant 7000 with 2 hard disks in a RAID 1 on a Smart Array 3100ES controller
3. Pulled the disks out and moved them to the NT 4 Proliant 6500 with no Smart Array.
4. Opened Disk Administrator and said yes to writing the signatures.
5. Powered down the NT 4 box and moved the disks to the Proliant 7000
6. Booted the 7000, watched as it saw the disks and all the data on them

So it looks like the Smart Array ignores the MBR and only pays attention to the config data stored in the first 4-8mb of the disk.