Save the factory exhaust and if you have an issue which allows you to re-install the factory system you may get away with it when you take it to the dealer.
Depending on the after market tuner you install, you may be able to back it out and go back to factory settings in the ECM but the dealer may find out when they hook their computer up. Then you are back to no warranty. If you don't perform your own repairs, this is probably not a good option.
Some people have cut apart the header, gutted the cat mesh, and re-welded the header. If cut at one of the existing welds and re-welded by an experienced welder, you can't even tell it's been messed with. Not the same performance as a new header though. Then you could use the Fullsac inserts on your mufflers as mentioned above and the bike looks stock. The tuner change can still be an issue.
As mentioned, you just need to decide which is more important to you, stock with warranty or modified for fun and noise. I had to remove my cat header because it was cooking my leg on my 2015. Had the engine rebuilt under warranty at about 26,000 miles. I then modified the bike and change the lifters every 20,000 miles or so. So far so good.