The fit is not that big a deal for a shop which can make a bezel. I'd approach Signature Audio in Scottsdale. They've undoubtedly had more experience with this than I have.
As far as the rest of it, there are shops on the East Coast which have replaced the HU but say that for servicing at the dealer, the HU must be in place so that the software downloading works properly. I don't know the details.
I suspect this is true for fiber optic cars only, but I am not certain.
If you want to know if your car is fiber optic:
If you have Logic 7, your car IS fiber optic.
If you don't, open the trunk and pull up the panel in the driver's rear corner of the trunk. Carefully examine the front outboard corner of the amp for a thick green cable. If you lack a thick (3mm?) green cable, your HU has an analog output and is not on the MOST fiber-optic bus.
If you do have a green cable, you do have MOST fiber optic at both the HU and the amp, and if you were my customer, I'd lean against HU changes.
For what it's worth, if you use the output of the amp, there is a LOT of EQing. If you use the analog out of the non-MOST HU and properly interface with it, the signal is clean and unmolested.
I've seen 06 E90s without Logic 7 and without i-Drive which were fiber optic, and I've seen 05 E90 without Logic 7 and without i-Drive which were NOT fiber optic.