Warranties are fickle things according to a friend in the business.
Some times all it takes is for the customer to come in all red in the face cursing the dealer and all those inside for the warranty to be "voided".
And another way... the person bringing in the vehicle "knows what is wrong" or "knows more about this vehicle than any mechanic", boom, sorry but the "limited warranty" does not cover this....
READ the warranties on anything you ARE GOING TO BUY, before you purchase said item, yeah they are long and lawyers write them, but you have to 'understand' them before you purchase, because when you sign that line, you are saying you fully understand the "warranty agreement".
If you work on an engine, or modify the engine, and your transmission fails... the engine is technically a part of the "drive train", so are any components "ON OR CONNECTED TO", the engine, "which affects its operation"... trust me, its in print, on the warranty, somewhere, on every vehicle's contract.... like I said, lawyers write these things.
Even if you just "add a cell phone charger", its draws current, from the electrical system, which is directly affecting the operation of the vehicle, and it was not an "option" originally for the vehicle, you could void the warranty.
I hate to be the dark horse, but if you are an ass, and are VERY demanding of a dealer, your problem is probably not going to be fixed if you have "modded" your vehicle in any way shape or form.
Now on the other side, if you talk to your dealers mechanics politely, and ask direct questions about a mod you want to put on the bike, you can circumvent the "warranty void". I always have had good relations with all the mechs and the parts counter guys. Some times I just stop in to browse new stuffs and look at next years bikes.
Get to know your dealers or the ones in the out lying areas.... I have never had a problem with any bike I took in, even though I heavily modify all of them with fuse boxes and outlets for charging, different seats, different suspensions and lighting.
And if worse comes to worse, you can always tell them "well hell, joe here told me it would not void my warranty!".... and joe will get the job of fixing your ride, covered under his warranty... LOL