Yes, I have read that paper. There are definitely two different, tightly linked genes that rarely cross over. (Laverty et al, 2018). They can be treated as mutually exclusive for practical purposes for simple breeding projects, but they are actually not.
One thing to note about the notion that this “should make it possible to separate them during breeding to grow plants without THC.” is that cloned CBDAS has been shown to produce small amounts of THC from CBG in vitro (I am having trouble finding this reference at the moment). These ezymes can be “leaky” which makes sense, given THCAS likely evolved from CBDAS. Different variations of CBDAS are likely more or less leaky than others. There is also potential that CBCAS also produces some THC.