Hi leeveney, I'm glad you're reading our docs!
Sometimes it's difficult to draw the line between what you could do if you really want or need to, and what you reasonably should expect to do. This one falls into that gray area.
As detailed in the Migration Tech Note, yes, you can replace a legacy UIO, EIO, or SIO brain with an EB1 or EB2 brain in a system controlled by a SNAP Ultimate I/O controller. However, please notice all the details involved--limitations, possible controller firmware updates and changes to the strategy, and the fact that you can't use new I/O modules with the EB brain unless you're running PAC Project, not ioProject.
The Current and Legacy Product Compatibility Charts don't have as much detail as the tech note; they are summaries based on what products you can expect to use together relatively easily. That's the gray area: what may be easy in one customer's application may be difficult or impossible (changing controller firmware, for example) in another application. In this case, we decided not to show EBs and UIO controllers as working together because of all those details. A dot in that box would imply that hey, they work together just fine! when in fact you need to be aware of all these other factors.
Hope that explains the discrepancy. I appreciate your pointing out issues in the doc, because sometimes there's a reason, and sometimes we just make mistakes. Bottom line, though, is that if you really need to do something, please ask. There may be a way.