Well, I'm back. Pro tip: don't necro 4 year old threads.
Passmark does indeed factor hyperthreading. I still don't have a motherboard for my X3470 because the board Amazon sent was defective. I still am not sure how Passmark calculates CPU score on multithreaded workloads, but observe Task Manager's Processes tab and you will see during multicore testing that if you have 8 threads you should have 8 Passmark CPU processes running and on 4 cores with hyperthreading disabled you should only have 4 - that's why your score may suffer.
Single threaded ratings are calculated on a clockspeed basis, at 4.1GHz your i7 is faster than an i5 at 3.8GHz.
The i5 7600 will only turbo on all cores to 3.9GHz which is why it has a lower score and having clock monitoring programs open while benchmarking seems to affect all-core turbo, which is something the user base for PassMark doesn't seem to understand, so their scores are lower.
A moderately overclocked i5 7600K can pull 10K+ in Passmark, and as you may have noted getting improved scores can prove challenging.
The reason new Intel chips can matched overclocked old ones is because of very little improvement in IPC. You want a cheap 6 core chip instead of buying an 8700K? Get a W series Xeon on X58 and overclock the ballz off it.
That being said about my X3470; I am still trying to get a good board for overclocking. It matches the i7 880 in cores, clockspeed, and cache. Basically the same CPU except supports more PCIe lanes and ECC memory.
Amazon's sent two boards and both have been defective, one had bent pins and the other just plain doesn't work.