I just upgraded from 4.1A (I knew I was running a 4.x but wasn't sure but that was the bin on my usb drive) to 5.3A. It took about an hour and a half to make it work (I had a ton of problems originally flashing the MS28) but figured it all out. So far everything seems to be working fine (backups, originals, etc).
I just wanted to post how I did get it to work in case anyone else might be experiencing similar problems (and also kept notes in case I need to upgrade again in the future).
Previous Configuration: 360 with MS28 drive flashed with Xtreme 4.1A
Current Configuratio: 360 with MS28 drive flashed with Xtreme 5.3A (Reporting as MS28)
Steps to do upgrade:
1) Burn Enable0800 is to DL DVD using Clone CD
2) Connect 360 SATA to PCI SATA Primary port
3) Connect PC SATA to PCI SATA Secondary port (not sure if this step was necessary)
4) Connect EIDE to PCI SATA EIDE port
5) Disable onboard SATA in bios
6) Boot PC (360 Powered Off)
7) Power on 360 (once PC booted to Dos)

Run mtkflash w /m x53a.bin (would not work with /SATA command)
9) Insert Enable0800 disc for 10 seconds then eject
10) Select mtkflash option for Primary SATA
Then it started flashing. My original problem (when using the badflash) was getting the menu in mtkflash. I think I had originally disabled all onboard controllers as that is what was recommended but I actually found I needed the onboard IDE enabled.
So anyway, so far so good. We'll see what M$ brings us with the update tomorrow and if / how it might affect any modded 360s. I am actually glad I did upgrade because my old firmware had the fall back to quiet mode when an original was inserted and I always needed to physically unplug my 360 for a few minutes for it to get to reset - now it is always running at full speed which is exactly what I had wanted.