I've been running a (HealTech) QS since new and haven't had any issues with trans (I'm @ 16K miles). But here is what bothers me what the dealer told you....
1) All dealers (in US) are privately owned and while it could be a 1 brand specific (Kawasaki in your case), the actual dealer isn't the one that approves or denies any warranty work (except for small stuff). They ALL call Kawasaki headquarters and submits their warranty claims and then find out if it will be covered (this is generally done over a phone call). So knowing this, its important that a local dealer has your back since they are giving detailed info on your MC (like mods, looks abused, ect..). They generally don't want to risk losing their dealer status. Some dealers use more discretion and are there to have your back and make you happy (to an extent) and aren't giving more info than is needed about your MC.
2) Legally, they MUST prove that a part you added was the direct cause of failure. Thats the law! (US only) Simply adding an aftermarket part will not void its warranty. While both the dealer and Kawasaki Corp can deny you, you can legally take it to court...its within your right. But I will add, it will likely cost you more time and money than may tolerate. I will also add that if you keep it professional, the dealer and Corp don't like to risk going to court. If your lawyer sends the dealer the papers showing they have been retained by you...they want to avoid if possible (rare it actually goes to a judge).
Here is what I would do. Don't buy any aftermarket parts at that dealer because they've already proven they will not have your back. If it was me, I would never deal with them at all. Buy the QS online and install it yourself or have another local MC shop install it. If done well, you can't see the QS unless you dig deep and are looking for it so bringing it to Kawi dealer for service they will likely never find it. Unlike all other quick-shifters on market, the HealTech has a really small and obscure pressure sensor that doesn't screw ----> QUICK SHIFTER HERE <-----
Don't let the dealer scare you, a quick-shifter comes stock on most SB's and has been proven to not cause ANY transmission issues.