Those timing graphs are completely irrelevant. They were made by Piru (a MorphOS developer), and do not compare like with like (the different versions were made on different people's systems with a different version of the software, probably compiled by a different compiler) - they're not comparing one system with another, they're comparing a truckload of variables, making the comparison useless for anything except propaganda.
It can be difficult to say which is "faster". On some tasks, a Sam 460ex will be better than a Pegasos II (for instance tasks which require better infrastructure - the 460ex uses PCI Express for starters). On others, a slower G4 Peg II will slaughter a 1.1GHz 460ex if the task is Altivec enabled.
I believe the order for most uses of AmigaOS 4 is:
AmigaOne X1000
Pegasos II G4
AmigaOne XE G4
Sam 460 1.1GHz
Sam 440 Flex and EP (faster CPU, 800MHz)
Pegasos II G3 600MHz
Sam 440 Flex and EP (Slower CPU, <733MHz)
AmigaOne XE G3
Micro-A1
CS-PPC
Blizzard PPC
Of course there are variations - I believe the fastest BlizzardPPC outruns the fastest CyberstormPPC, for instance. Then of course some apps use the faster bus of the Sam compared to the AmigaOne XE, that sort of thing.
Generally speaking, though, the Peg-II is a good board to have if you don't mind being limited to pre RadeonHD graphics cards and a PCI/AGP bus. If you want to run more modern graphics cards you need a Sam460ex or best of all the X1000.
