Hey, you are a familiar name on the e46fanatics board...
I also retrofitted my car recently. I took it to the dealer for recoding but my tech told me that the retrofit is not a US option so there wasn't much to recode. The automatic scan just showed a bunch of errors. They cleared the errors caused by the installation of the nav unit and said I was good to go. Seems like everything is working on my car so I can't complain. Note that my car had assist from factory (It already had a GPS antenna connected to the TCU) I don't know if it makes a difference.