Definitely keep the error checking on, it's there for a very good reason, actually the main reason why the 3D models exist to begin with, they are not just for decoration. See what parts collide and fix it. Then you know you can actually build it (assuming, the 3D models match the reality)!
If the desired thermal connection between the heatsink and the chip is causing the error, add a custom rule for those particular parts, allowing zero or even slightly negative mechanical clearance. This is better than turning off error checking completely.