Every description of hard drive partitioning schemes I have ever come across defines secondary partitions as areas of the hard drive outside of the primary boot area. The boot area will be the fastest to access in every case and therefore the best place to put files that you want fast access to would be the primary partition. That being anecdotal evidence I have actually tried this and I discovered that using a secondary partition will slow down access and over time things just get worse and worse. That said you may not notice this at first with AHII because the hard drive accesses seem to grab much smaller data chunks than do programs like FSX using photo terrain images.
How much do you want to read? I could write about three pages on how to setup W7 for flight simulator X which will also make sure the system runs AHII more than fast enough.
I can't say anything about FSX but AH2 needs little to no disk I/O during gameplay. It will load some textures occasionally most likely but that's it. Partitioning will have zero effect on gameplay. Comparing AH2 to FSX is comparing a mouse to an elephant.
The slowest part of a 1Tb 7200rpm drive will still be loads faster than an older smaller 7200rpm drive at its fastest. Not to mention that partitioning per se has nothing to do with using the inner areas of platters - they will be used eventually when the disk fills up no matter what. So it's really not worth even thinking about.
I have always partitioned my drives in several chunks and I never suffer from any performance problems. Quite the opposite.
Now, factually what you said is true. Partitioning will split the disk and the secondary partition will be on the 'slower' part of the disk. But the gaming experience is not dependent on it. The difference is negligble. People should concentrate on things that matter and stop digging for trouble where it's the least expected.
If games would constantly access hdd no game would run properly. There's about 1000 times performance difference between ram and hdd.