Any question answered...

To add to this; I just took the top cap off and loosened the stem and there was a significant amount of wobble, around a degree or two I'd say. So seems like the stem bore is slightly larger than 1 1/8 (or the steerer is small, but this seems less likely as the spacers are quite snug.

Here's a pic:

Just went into Giant this afternoon, they agreed that it was a manufacturing default, as the same bike on the shop floor didn't have that issue. They didn't have any spare 90mm stems in, so gave me a 100mm for the time being and have ordered a new one. Also gave my wheels a quick truing whilst I waited. All in all, good service.