When I was shopping for mine, I saw a lot of those prices, too. When I bought mine this week, this was the breakdown.
MSRP : $39,090
MojoMats & Trunk Liner (Golf R labeled mats) : $235
Roadside Assistance Kit : $85
Destination: $820
Total: $40,230
Anything that's $40,145 is likely missing the roadside assistance Kit.
I can also confirm that the Golf R labeled Mojomats are significantly nicer (thicker, softer, and more durable looking) than the stock mats.