My understanding is the same.
When I upgraded my ECU software on my E39 M5 - I chose Powerchip. Great software.
Powerchip assured me software changes is transparent to BMW dealerships.
I was able to confirm this when I had to take my M5 to the dealer to update stock ECU software post Powerchip tune in order to address a BMW service bulletin.
I took my car to the dealer, they uploaded latest version of BMW software on my M5.
Dealer never mentioned anything about software tampering.
Once I got my M5 back from the dealer - I had Powerchip reload their software again.
Zero issues on the above.
On my M6, I contacted AA prior to going forward with their software tune.
I was assured the same - that software changes is transparent to BMW dealership.\
And if I had to take my car back to the dealership for BMW software update - AA will reflash my software back for free.
However, if you call your dealer and ask them if aftermarket software upgrade will void the warranty - you can pretty much bet their answer would be yes.
As I have posted here and going through 2 software tunes already on 2 different cars - I will not go back to stock software.
Just sharing my thoughts and experience. We each take risks in our daily life and my experience may be different than others.
The dealer cannot tell that the ECU has been modded unless your ECU is sent back to Germany. They are the only ones who can see if it has been tampered with. So unless you have an engine breakdown, and they have a feeling that you have tampered with the ECU, and decide to send it to Germany for testing. You should be more then okay.
It won't void your convertible top warranty, or anything else unrelated to the engine for that matter.