On the surface I would have to agree with the comment about getting a job at the Gap. Depending on your goal, there are stock bits that arguably should be replaced, some that probably should not, and some for which it won't make much difference. Depends on the item, and how you use the bike. Your desire for Max horsepower, torque, durability, aesthetics, comfort, etc., are what drive that equation, whereas stock parts are about profitability, emissions, and that sort of thing.
But there is the goofy stuff we consumers sometimes buy and slap on the bikes, and when the bike goes in for service at a dealer, they are stuck trying to figure out the source (smoking gun) for a problem the bike may have, which can obviously be complicated with the addition of non-stock parts. They, the dealer, can't be responsible for every little mod and non-stock item that comes along and how it effects the bike, so many dealers just steer you away from them.
All that said, I've had fine success with K&N oil filters on multiple Ducatis over the last 20+ years, including my current 1200 Multi. Are they better or worse? I'm not touching that, but they are at least ok, and of course lower cost if purchased smartly, versus an OEM Ducati filter from the dealer.
My (AGM) non-lithium battery has not given me any issues (knock on wood), so i leave it be. The idea of the lithium battery is appealing, but the reality isn't appealing enough for me just yet.... too little gain for the number of potential issues. But that's just me, and lots of folks have had great success with Lithium batt's.