I'm not sure about where you live, but here in the US there are legal protections for consumers (Magnuson–Moss Warranty Act) that says modifications cannot void the warranty. However, a warranty claim can be denied if it is found that your modification was a cause of the failure. In other words, if you flash the ECU and later have a gearbox failure that should be covered by warranty, then it must be because flashing the ECU has no bearing on the operation of the gearbox. Again, that's in the US law... the manufacturer or other jurisdictions may have different opinions of this.
I wouldn't be surprised if new-old-stock Centenarios continue to be available at dealers for a while, but I wouldn't guarantee it. Guzzi has a bit of a track record of special editions lingering around in dealer stock for a while. Its a gamble. As for the seat, yes... spare parts Centenario saddles should be available from dealers.
__Jason