HondaCare is good stuff. My bro is a Honda tech and he has seen it pay off for ppl time and again saving big $$. He recommended that I purchase it.
Also, it's supposedly illegal for a mfr. to void a warranty just because of mods. The mods have to be proven as the cause of the failure. With 3rd party, I'm not sure if the law still applies...IMHO they jacked your bro-in-law. Bigger tires is a poor reason to deny coverage. The problem I think, is that certain dealers are more rabid about denying modded cars than others. They can always claim that failures were due to a modification, and the owner has to push the issue if they think they're in the right. If it's a big enough issue (especially with a Honda) a person can call Honda themselves and raise a stink.
BTW, I paid $1k for my mine, 7yr./100k miles. I would strongly recommend it to someone with an auto. trans. The cost of that alone to replace would more than pay for the warranty.