@OEM+ DUB on here uses Golf ball joints on Passat alloy wishbones without an issue
As he told me, you just need to make sure you use the Passat/S3 shouldered nuts.
The difference between S3/Passat and the Golf BJ looks to be roll centre correction? The tapered pin is longer on the S3 ball joint, because I assume it's ride height is lower than the GTI's? This will correct bump steer.
You could, and probably should, use the S3 ball joints on a lowered Golf?
I've got the Passat wishbones and bearing housings also, and brand new Golf ball joints from VW ready to go. But I'm thinking the same as you now, should I switch to S3 BJs?