Forum members weighing the option of simply swapping speakers v. adding a 3rd party amp such as Bimmertech will want to stay in touch with Zooks527's account of his experience with a dealer ECU flash that failed, very likely due to the incompatibility between the flash and the circuitry of the 3rd party amp, with the result that his car was (temporarily) bricked at the dealership.
Zooks reports that the 3rd party amp provides better amplification than the stock amp but that, at least in the case of the flash he received, the flash would not have failed if he had swapped out the 3rd party amp back to the OEM amp before the visit to the dealer. Zooks reinstalled the 3rd party amp after the flash with no apparent negative consequences.
So, on the Boo-Hooray evaluation scale, we have:
3rd Party Amp:
Better sound (Hooray)
Having to swap amps before and after visits when a flash is due (Boo)
Risk of flash failure & bricking the car if you don't swap the amps (Boo)
Speaker Swap without 3rd Party Amp:
Not having to swap amps (Hooray)
No risk of incompatibility with the flash (Hooray)
Worse Sound, perhaps (Boo, perhaps)
For further updates on this, it would be a good idea to check in on Zook's thread at
http://www.2addicts.com/forums/showthread.php?t=1260271 in case there are more developments.