I don't know if BMW 'knows' more about newer cars. However, don't cut wires with your retrofits. Either do pin-to-pin additions to your harness or create a PnP patch harness. These are very simple to do if required (usually less than 10 wires) and just good practice really.
If something does happen, as with anything don't take chances or give someone the chance to say your diff broke or wheel bearings need to be changed because you coded your music list to be visible in your HUD :roflol: Revert to stock config. Also as zaleonardz says above, don't claim for stuff under MP that your car didn't leave the factory with :roflol:
Although simple FDL coding is not an issue (provided you aren't changing VO, date of manufacture etc). Don't go too crazy under plan. If your car needs coding by a dealer in future, your FDL values will all be gone, but also depending on what you've retrofitted the car may throw errors (probably not for paddle shifters but if you have retrofitted things like driver assistance stuff or surround view etc. Some also may not throw errors in daily use but will show up as an uncoded module on the dealer systems (My iDrive touch retrofit for example showed up as such initially despite working perfectly)
Happy coding
I am glad to see more people eg: Holiman, Phoenix yourself and a few others are increasing in number and not afraid to play with technology

I try to learn about the electronics and software as I plan to own more than a few of the cars of this and future generations. You also never know what life will bring you and having knowledge or skills can be useful in future.