The exact same things happened to me. I brought my 1299S in for it's first 1000km service and I had the akrapovic exhaust put on.. I thought damn it's loud and I came back to the dealer the next day to ask if they can put the baffles back in. They said it's cooler to have them out and it will sound like a standard exhaust if I put them back... well 5 months later and 5000km I decided to bring the bike back for an early service. When happened next is they found there's barely any oil in the bike, I was very surprised. After a few faults needing fixing I got my bike back 3 weeks later... So the bike now has oil and doesn't sound as angry it's actually very bearable not making my ears bleed anymore. I've just visited family and the they said the bike is a lot quieter. When I got the bike after 1000km it didn't have enough oil that's why it sounded so loud and angry. The dealer gave it to me that way and I always thought it was just the damn exhaust. I didn't get a low oil light so I had no idea and somewhere in the manual near the back it says to to check the oil.. I was checking where I knew. Ducati should show you when you get the bike .. they should give you a daily check list before you start riding.
This is the sound of my bike before the 5000km early service..
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