They include all data that they are given access to. This is not "massaging data" this is presenting the data they have. So you're saying because a particular publisher doesn't give them digital sales data they shouldn't bother posting the list at all?

The reason PUBG isn't higher on the list is because the publisher doesn't tell NPD it's sales. The reason Nintendo isn't higher on the list is because they don't tell NPD their digital sales. This isn't NPD's fault or NPD massaging the data to put their favorites at the top.

Their is literally nothing NPD can do about that, it's up to the publishers like Nintendo.

Id say its pretty obvious NPD wants to make certain western devs look better.

During Wii and DS gen Ninty games were dominating the top 10. What do they do to change this? They combine the SKU's for games.

For example they used to list Call of Duty separate for each platform. That way it was easier for them to fall off the top of the list.

Yet they continue to separate Pokemon games when other trackers combine them. Mainly Nintendo themselves 

Pokemon versions being separate is a point I agree with, they should be combined. But that's just one game.

Combining sales of multiplat games just makes sense, and it's not to make "certain western devs" look better. They combine mutliplat releases regardless of where the game was developed. Japanese titles like Monster Hunter and Resident Evil are also combined. While western developed single-platform titles are treated the same as non-western developed single-platform titles.

it makes sense not to include mobile sales because then you would have 99 cent games all over this list. I wish they didn't count them on the top 50 best selling games of all times because Tetris by EA is number 3 on the list with 100 million selling at 99 cents for most of its run which isn't fair to the 40-60 dollar games while some can beat it out most can't because at the end of the day they aren't minecraft or GTA V but they have made great sales and should get credit for it not these mobile games.

It's poor analysis.  A better list would only include physical sales.  Then you'd be comparing apples to apples.  A list where some of the games have all physical+digital sales and other games only have some or none of the digital sales is a poor list.

It's like holding a marathon, and then when the race starts some of the people bring bikes.  The bikers say, "should we be punished just because they didn't bring bikes?"  So the people holding the race let them use bikes and the others run.  That's not a fair race.  This list given in the OP is not a fair list and really none of the NPD lists are fair anymore.  Some of the games include all physical and digital sales and some don't.

Also, yes the NPD does "massage" the data.  They used to be a lot more transparent, giving both hardware and software numbers, and they also used to report each game on their lists as a separate SKU.  The format started changing once Wii games were filling up the monthly top 10.  The bias is obvious, because they started combining third party SKU's, but they never combined the Pokemon SKU's.  It was a move to make third party companies look better.  The NPD is a business and some of their clients are large Western publishers.  They definitely have a financial incentive to "massage" the data.