Unless you are putting down 300HP+ to the ground, a properly-mounted torque strap won't do any damage to the subframe or exhaust manifold. And if you ARE putting down that much power, you'll need one anyway to keep your engine from crashing into the radiator and/or firewall.
I had some doubts about the mounting points (particularly the exhaust manifold) but it seems that many people have put a lot of miles on their torque strap setups with no ill effects. It's just a matter of time before I'm up under the engine and decide to strap the Yamahammer down. Quite frankly, I'm surprised the factory mounts have lived up to 20K miles of tire-chirping, whiplash-inducing 7200rpm shifts.
Once you throw your first set of motor mounts, you'll be more inclined to use a torque strap.
