Forget the user's guide. It is most likely a bug. I don't have a solution but I do see the problem. It appears to be a few bugs related to page layout for printing. I didn't bother printing to paper, only to PDF, but it is supposed to print what you see in the print dialog so I assume it will do the same thing whether PDF or actual paper. This is an embarrassing mistake on something so fundamental.
Having page headers "repeat" on every page makes it worse but the problem is present even without that. With "repeat headers" off it appears to misplace 1/2 row of space per page, but I can't be sure that's exactly what is going on. It misplaces an additional row's worth per page with "repeat headers" on (one per page for each header row). The size of the page headers and footers and page margins also move Table 2 around.
Go to the Numbers menu and choose Provide Numbers Feedback to report this bug. I will too. I have my doubts they'll do anything about it but it is worth a shot I guess. Adding new features appears to be much higher priority than fixing bugs. I wish Apple would reinstate their old slogan of "it just works" vs "it almost works, but forget that and look over here at the shiny new features we added".