Depends on what your mod is. If you drill holes in your exhaust, you can kiss any warranty on the exhaust away. If you change your headlight and something happens to the lighting then it would be under warranty if a dealer did it. If you did it it may still be under warranty, but they could refuse. I know some will post back that a dealer doesn't have to do the work, but the company can claim unless your qualified then something you did may have caused the problem. Reverse wiring etc. But on my last bike I had a 3 year warranty and never used it once. The bikes today really are trouble free.
The most important thing is to have a really good relationship with your dealer. They are the ones who will be doing the warranty and they get paid by Yamaha. So they won't care about doing the work under warranty and claiming its factory problem if they like you.
The most important thing is to have a really good relationship with your dealer. They are the ones who will be doing the warranty and they get paid by Yamaha. So they won't care about doing the work under warranty and claiming its factory problem if they like you.