The only thing that has to be taken care of, is not using AFCADs that are distributed with traffic packages, because those are usually made for the default airport and always use the AFCAD we supply with the scenery and, eventually, remove the one that comes with the traffic package.
Note that this, even if it will affect GSX it's not really a GSX issue: if you have a traffic package with its own AFCADs, it would be best to remove them even without using GSX, since they would create issues (positioning problems, taxiways problems, AI problems, etc) to the scenery itself too, without considering the GSX issues.
Other than that, there are no other issues. We use Ultimate Traffic to test our sceneries with AI.