Will the 2 joining pieces be made out of the same material (plastics)? Each material has a different shrink rate, meaning that if the 2 parts will be the same material the tolerances for both can be the same. If they are different materials you have to take into account the rate for each material and place your tolerances according.
I think for plastic parts shrinkage is something that needs to be looked at tooling level. The best strategy to adopt is make sure your parts are producible get DFM analysis done before you freeze your specs. Post DFM focus on tolerance and see if it fits vendor capability. A holistic approch is required when dealing with Injection Molding. Shrinkage is something which depends a lot on design and process parameters as well!!!