I am the guy making the reading order, and it is not in publishing order. It is fairly chronological, but groups story arcs together so you aren’t jumping from one story to another then back to the previous arc, or in the case of some chronological orders breaking books appart so you are going back and forth.
The WWII stuff isn’t in as of now, but there will be an “earlier suggested order” added later where those will be available to read. Stuff like wolverine origins will go closer to their publishing order but marked as flashback, since reading those then reading a book from the 60’s really breaks the intent and meaning of those early books. We (a lot of people in the forums there are helping to fine tune the parts of the orders are done) are trying to make it so characters are where they should be at a given time, so if thor is off on asgard and hasn’t returned you don’t then read a issue where he is in new york with the avengers. The goal is to make it a real reading order.
There are also tools there so you can build you own reading order with just the groups/characters you care about, or read the only the books from the order featuring a specific character/group/story arc. You can mark books you have read and it will then feed you the next book in the order, and issues that are available through Marvels Digital Subscription service have links to that so you can quickly get to them to read.
Hope you guys stop by the site and the forums there, say hi, and start reading some marvel comics (as of this posting we just hit 1980).