No, he means that the backside of the PCI cards' circuit board faces upwards, instead of the component side.
That's exactly as it should be, it keeps the majority of settling dust just lying on a bare board, instead of clogging up the components. It also keeps the area next to the RAM and the CPU socket free from any intrusions from the first PCI-e slot. Many motherboards are EXTREMELY tight, and on some, you have to remove a video card to get the RAM in or out. Can you imagine how tight it would be if the components (and therefore the cooling system) was sitting on top of the PCI-e slot? You woudn't be able to fit a decent CPU cooler at all.
The only downside I can see to the current system is that passively cooled graphics cards (like my Gigabyte X800XL) have to have heatpipes to get the heat round to the "top" of the card, in order to effectively radiate heat away. This **does* encroach into the CPU cooling area, but my Thermaltake Sonic Tower passive CPU cooler fits without issue.
This is a legacy thing, from way back, and it aint gonna change any time soon - not even with the BTX form factor.
So just get used to it.