You shouldn't have a problem as long as you aren't running the bullet into the rifling, which could cause excessive pressures. You'll actually see better accuracy sometimes with the bullet set just off the lands. As long as it feeds fine in your particular rifle and you are getting the accuracy that you like, you shouldn't have a problem with it. Remember that a lot of bullets don't even have a cannelure.
If I am loading one round for several rifles, then I will seat to the top of the cannelure, and measure to make sure it is within SAMMI spec. Those factory loads have to be able to fit in every factory rifle out there.
Yes, I'm trying custom fit the cartridge to specific rifle. What I did was seated a bullet in an empty case and chambered it to find the lands (a trick xring taught me) and then seated the bullet another .020" deeper. They chamber fine and the accuracy has been good. This is the first bullet I've loaded that has a cannelure and I wanted to make sure I didn't needed it seated into it.