I'll add my success story as another data point...
I was running a pretty stock 4.5.91 image, sim unlocked, bootloader unlocked, rooted Atrix with hotspot change and a few other tweaks.
I used RSD 5.6.4 to flash over my install:
1FF-olympus-user-2.3.6-4.5.141-111212-release-keys-signed-ATT-US-GAS_NA_OLPSGBATTSPE_P012.sbf.gz
md5 checksum of the gz file is 78cbe2314d76016a12118b30655a3451
md5 of the extrated sbf is 0bc556a7fd949317f061e29d88632242
I then used Automatic Bootloader to re-unlock my bootloader even though I think it stayed unlocked from before.
Lastly, to finish up I used the preinstall root method to regain root.
I then used my existing install of ROM Manager to reflash clockworkmod recovery, booted into it and wiped the davlik cache and battery stats, might have wiped the cache as well.
In the end I am running an unlocked bootloader, rooted, 141 and I kept all of my apps & settings including the hotspot edit.