As stated earlier I've a CRS 3.0 City - slightly higher spec than the CRS 4.0 (your second option above) and the "City" means guards and pannier rack included (like your first option) . I love the mudguards that came with it.
Mudguards have thin rods that go from the axle to the mudguard to hold it in place. On the Giants own mudguards, this rod is a single rod that wraps round the back of the mudguard and does both sides of the wheel. On after market add-ons, the rods only serve one side and are too long and poke through the back of the mudguard (designed to fit different sized bikes at a guess) and need to be cut off/trimmed down.
Both my old bike and my wifes bike had mudguards added after buying them. I was never keen on the sharp bits of metal sticking out of the back of the mudguards and managed to stab my shins on the front ones once during an off.
Its not a big point, but if you can't choose it might help sway the decision.
(Also, if you can get one of the Giant bikes locally - can't the shop order in the other and let you test ride it? Tell them you can't decide between the two - and that you'd prefer to test ride both and buy from them than to buy over the internet without a test ride. Most LBS's should be happy to ensure you get the right bike and should see the opportunity to build some customer relationship - they want you to come back for servicing, parts, clothing, extra bling, etc... and a little help getting a bike goes a long way and they may match an internet price or bung in some free accessories.)