yeah slip on. The reason I'm not getting a full system is because I don't want to void my warranty in any way so I'm not touching the flies either (I'm of the mindset that they are a part of a system I paid a lot of money for) but 3 years isn't a long time..
Replacing the exhaust does not void or jeopardize your warranty. And don't let any dealer try to tell you that either! And you don't need to touch the secondary butterflies when replacing the exhaust system. But it makes sense to change their behavior (by removing them or reprogramming them) and that can be done with a reflash without touching them. Now, reflashing could be argued to more likely to potentially affect warranty, in theory, but they can't detect it is done, so it should be moot.
Generally, the manufacturer cannot deny mods, aftermarket parts or addons, etc... and if they want to deny warranty work, it is up to them to prove that your parts or mods
caused the problem that needs to be addressed by the warranty.
Do you need to have a bike with that exhaust to set up a tune or is there a general 2015-2016 2BROS tune that will work for most slip on bikes?
If by "exhaust" you mean "muffler", those don't affect performance in any meaningful way and so there should be no difference in the tuning/flash. But if you replace the exhaust [system], that will require a different tuning/flash. I don't know which Steve has done or not done so far; but he will absolutely need access to an actual bike with those mods to create a tune.