If Genesi uses the MV64361 controller then why do the only have one Gb ethernet port
There's only enough space on the back for a certain number of slots and sockets. There's the original VIA Rhine ethernet device there for compatibility with everything else.
and why no PCI-X slots?
Do you know where to buy any?
If the answer to any of those is "no", then this is why you do not need PCI-X slots, and why they are not provided. There is also the issue that PCI-X slots are longer than PCI slots, and there isn't enough space on the board. Anyway. You don't need them.
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As for other stuff: AGP 1x is fine.
There is no game on the planet that does a forced AGP transfer for texturing for every frame, unless it is starved of video memory. With a 64MB card, this doesn't happen very often.
The same can be said of vertex buffer objects, which means that certain transformable vertices (i.e. raw data to be manipulated by the tnl engine) can be stored in video memory anyway, saving transfers for whole swathes of vertex data.
A PCI Radeon or GeForce 4 card performs identically to the AGP versions, apart from initial texture loading (maybe at the beginning of a level.. that progress bar will stay for longer) and in starved situations.
Quite rare these days unless you're running 32bit 1600x1200, 32bit Z-Buffer, 8-bit Stencil buffer, 4xFSAA, and have 60MB of raw texture data.
There are texture compression techniques which can be employed, Z buffer compression techniques, and many other things, which means most AGP-capable cards rarely touch the AGP bus because in fact it is highly discouraged

AGP 8x and so on is a pandering to the onboard chip manufacturer, where video RAM *is* system RAM and is *always* transferred across the AGP bus. If you noticed, these chips allocate some pitiful 16MB (4, 8 are not uncommon either), and are also very common on most motherboards anyway.
With 133MHz DDR (i.e. DDR266, PC2100) memory you can saturate your AGP bus completely with those rates. Now that most PC motherboards come with DDR400 memory capability, dual channel options, AGP becomes a slow tortoise to the memory's rabbit.
Slowly but surely, it gets there. Since upping to 8x is easy and gives Intel and SiS and VIA something to increase the speed of their commodity internal graphics architectures, they did it.
That doesn't mean it makes a great deal of difference to your Radeon. As such, it makes barely a difference to the Pegasos.