From a recent buyers perspective...
I spent ages looking for 'the right' GSA. My major (or only real) consideration was condition, mileage and service history. There were certain colours I didn't really want but I'd have lived with it for the right bike. Luggage was definitely a 'nice to have' and as most GSA's were sold with panniers - I pretty much expected them to be present and I didn't expect to be paying a premium (although again, it wouldn't have stopped me for the right bike). I didn't care at all about any other bolt-ons - I pretty much expected to have to buy some bits to make it how I wanted.
I ended up buying a just about bog stock 2012 4000 mile TC from a dealer just before Christmas. It came with panniers and a swingarm crash bung (and a
nippy Norman oil bottle which I discovered later 'went missing' during it pre-sale service...) but nothing else. I was more than happy with that.
I then bought some (what I thought to be 'must have') bits and pieces - oil cooler guard, crud catcher, mudsling, fender extender etc. and I bought these new as because the bike was just about good as new, I wanted new 'stuff' for it (sad, I know... ). I also bought a second hand gsa top box and mounting rack.
So, the upshot from my perspective is - I'd say if you can be bothered doing it (and then ebaying them), strip the bolt on bits from the bike - it probably won't matter at all to the buyer. However, luggage will definitely increase it's appeal and you could probably charge a few hundred quid premium in a private sale for OEM panniers.