yes, basically sisoft, which also had issues reading bandwidth on nf2, and maybe intel's first dual channel, can't detect/doesn't use the 2nd connection. now if this is effecting some other benchmarks and some things aren't using enough threads is questionable, i don't think its an issue really.
as for cache, core 2 duo uses massive cache to counter latency, to a point, k8 also used little cache, thats the design of the chip. core 2 duo wouldn't work great with 512kb cache per core, and phenom's most likely would get little extra speed out of 12mb cache.
as mrthingyx pointed out, you will rarely be able to see the difference. in games, there is NO difference, the biggest difference will be 4-5% in sup commander or something, in 99.9% of games fps difference will be 2% max, and no, you can't feel that.
you could take the CEO of intel, or maybe better bet is the head designer. blind fold him, get two computer to the start of first level of crysis with identical setups except one being a phenom and one being a penryn, and he wouldn't be able to tell you which was which. you could run the same test with a 2.4Ghz phenom vs a 4Ghz penryn, and a 2.4Ghz penryn against a 4Ghz phenom, or a phenom/penryn at 4Ghz vs a dual core at 2.4Ghz and again, the guy wouldn't be able to tell you what cpu he was playing on.
as far as it goes, for 95% of us, thats the end result of which chip you buy. i've got a couple intels, i'm switching one system for a phenom, probably my main overclocking/gaming rig, purely because i want to play with it. i know it won't affect my framerate in the slightest.