:"you will see the AGP card off a PCI Bridge off the main PCI bus." Just because you see something doesn't make it real. PCI was built on the assumption that there would be a root PCI bus with devices either directly connected to that bus or connected to it by bridges. More recent systems don't physically follow that topology but they still have to pretend to follow it for compatibility reasons. 
 :"Updated 5V TTL (S, LS) and CMOS (HCT) logic levels were .4-3.5 out." you seem to be misleadingly representing maximum zero voltage and minimum logic one voltage as a range of voltages. When connecting stuff together you have to consider maximum logic 1 voltage which for outputs is usually specced to be the same as power supply voltage and for inputs may or may not be greater than the supply voltage.