The ATX form-factor supports up to seven expansion slots. The spec I found is ATX 2.0 and they only mention:

These slots may be any combination of ISA, PCI, or shared ISA/PCI.

and the diagram doesnt show any AGP slot as well. Since the slots have to have a 0.8 in spacing I'm guessing one of the slots could be AGP or PCI but had to maintain the same spacing to meet the ATX spec.

Unless I'm mistaken the Abit board you show has a shared ISA/PCI slot.

(edit) I didnt look up the SE440-2 spec before posting and see it also has a shared ISA/PCI slot so not sure why intel put less slots on then the spec allows. So no help I guess.... shrug.

I've noticed this as well. Intel's boards were known for their stability. Perhaps they felt a seventh slot on their reference boards, while part of the standard they wrote, was unable to be driven reliably enough for their elevated quality control.

Stability and idiot-proofness. Intel mainly sold to OEMs and they wanted trouble-free operation. Given there are only four interrupt lines on the PCI bus and despite spec saying cards should play nice and share if needed, a lot of cards don't. So on boards with 5 or particularly 6 PCI slots you frequently had to juggle cards around to find which cards really didn't like to play nice (usual suspects: SBLive, add-in IDE/SATA, TV cards etc) and which slots were unshared. Not a major chore if you know what you're doing and why, but if you don't and assume all PCI slots are equal, you can get into a bad frustrating mess which Intel's customers don't want.

Of course PCI shares with AGP and with integrated I/O as well, plus the BX-6 shown in comparison also only has 4 PCI slots, so that's not the difference here. The other difference is clearance around the CPU slot. By not using the top external slot position, Intel allows for more distance between AGP and CPU, and between CPU and top of case. That not only allows easier CPU installation, but also allows OEMs to use creative shrouded cooling solutions that wouldn't fit if crammed in. IIRC Dell, who used the SE440BX, used something like that.