But there's still two days left for this month. I can't see the sense in this.

Last year's NPD was 4 or 5 weeks?

I think they want to keep the NPD months as 4 weeks-4 weeks-5 weeks, which makes things tidier really. You never get a proper calender month of tracking.

4. NPD reports go like this: Jan+feb 4 weeks, march 5 weeks, april+ may 4 weeks, june 5 weeks, with that pattern (two months of four weeks, one month of five continuing).

So it's almost done for this month.....

GameStop has NDC bundle twice as the best selling console.. 1 is NDC but out of stock on their online store (it is in stock in retail stores, I checked their page on that), then the other shows as a pre order released on the 4th of December, which I assume means that's only when the online store will replenish its stock of the bundle.
These guys want people to go to the actual stores so I wouldn't be surprised if there is artificial limits on online availability. Either that or online shopping ratio exceeded expectations and stores didn't have enough stock compared to retail

2 hours since last update:

#01 PS4 Nathan Drake Bundle (same)
#04 XB1 Gears Bundle (same)
#20 XB1 Three Games Bundle (down 2)
#23 PS4 Star Wars Standard Bundle (same)
#45 3DS Mario Land Bundle (down 2) [out of stock]
#55 PS4 Black Ops Bundle (same) [out of stock]
#85 N3DS (same)
#87 PS4 Nathan Drake Digital Bundle (down 5) [out of stock]
#91 WU Mario Kart Bundle (up 8)
#95 XB1 Fallout Bundle (down 4) [out of stock]

PS4 - 4 bundles, 4 in the top 100
XB1 - 7 bundles, 3 in the top 100

XB1 Deals:

Gears Bundle ($300)
Halo Bundle ($450)
Kinect + Three Games ($466)

PS4 Deals:

Nathan Drake Bundle ($300)
Nathan Drake Bundle + Star Wars ($358)
Nathan Drake Bundle + Fallout 4 ($358)

I thought this month was a 5 week job, seems weird to split the month in the middle of this weekend.

I meant game changer for this weekend only in my post. As it usually features heavily in the PR for everybody. For the rest of the month, I don't think it was close. Looking at last month, I would say rather than losing to the XB1, the PS4 lost to Novembers PS4 bundles instead anyway.

Not only that, but Black Friday weekend.

The Amazon deals are now Cyber Monday so I think that ND bundle can stay at #1 until Monday night.