Theoretically, a carbon fork will absorb more road vibration, making it more comfortable on your hands / arms when you ride on rough pavement.

Aluminum on the other hand is a very stiff material, but will not dampen that much, so you feel all the bumps and cracks in the road more.

Will you notice a real difference? I don't know. But there must be a reason why many manufacturers use carbon forks on entry level bikes, even when the entire rest of the bike has no carbon on it.

Also, my old 30yr old full aluminum Cannondale STILL has a steel fork, because steel absorbs more vibration than aluminum. So manufacturers seem to have shied away from using aluminum forks for decades. If that tells you something...

For a noob: doesnt matter if you are a noob or an experienced rider. Everyone feels comfort.
Personally, all things being equal, I would definitely go for the bike with the carbon fork. I would spend $100 extra on it probably. That being said, the general fit of the bike is more important for comfort, so make sure the bike fits you properly first.