Like hell they will. My 4runner had a squeak from about 5,000 miles. Somewhere in the front end. I later installed a 2" spacer lift up front.
When I went in for an oil change, I asked the dealer to look for the squeak. They told me that because I had modified the suspension, and scraped a lower control arm and dented my gas tank skid, that they would not diagnose it under warranty. I would have to pay then their time, which would be refunded if they thought it was Toyota's fault, if they found anything.
I told them to pound sand, went home, and in 5 minutes figured out it was the hood.
If a rod goes out after an SC install, Magnuson and Toyota will point their fingers at each other. Nobody is stepping up for that new engine bill.
It will be up to you, the owner, to prove who was at fault. Expert testimony is EXPENSIVE.
I am not sure you are familiar with The Act. The one and only place "Magnuson-Moss" means anything is in court. By the time you get to court, you have already lost. Can't get there for less than $50,000. Not including the expert working up its case. Toyota will have an expert, and did will the SC mfr.
Even if you keep it in small claims court, which judge will accept that putting a blower on a motor didn't cause a rod failure? Toyota will point to their reliability record and that's it.
"Magnuson-Moss" will not help here.