If you're booking the cabin you want to fly in, and it's priced sanely, there isn't much of an issue.

The problems tend to be related to upgrades (UA xxx operated by AC cannot be upgraded until day of departure, SAUA cannot be done on codeshares, etc.), or YYZ-TYO in J and then a codeshare to SIN in Y, on a J fare.

On the YYZ-SIN example (one I've done a lot of research on lately), AC.com always wanted to put me in Y for the codeshare connection. It was possible to book through AC on the native flight number in J for the same price, but it required more work.

And then that becomes my next point. It's often easy to book the true flight number for the same price. So just do that

But if you recognize the issues and are fine with them, I wouldn't worry. I've flown a bunch of UA ticketed UA marketed AC flights, and I've never had an issue.