Indeed the nMP has some real limitations on the implementation of both USB3 and for that matter ThunderBolt.
The USB3 implementation is as you say hamstrung via a single PCIe 2 lane. Adding lots of high speed drives to each of the ports will saturate the bus.
Many people see the individual ports and assume each has a separate controller and bus bandwidth. Not so, it is a shared bus for all available ports. In fact Ivy Bridge does not natively support USB3, Haswell does though.
Likewise the 6 TB2 ports are configured via only 3 controllers and HDMI shares bandwidth on one of the controllers/lanes(3). Furthermore, due to limitations of TB2 this is limited to 4lanes of PCIe2 for each controller, but there are only 8lanes available and the nMP uses a switching chip to allocate the needed bandwidth. Add in the shared HDMI and hook up a 4K monitor and you will really see some performance drops. Everyone that is connecting drives (raids 0)s should be sure to balance the loads on the controllers.
Bottom line is that current TB2 has some serious limitations on theoretical thru-put.
I think Apple erred on how the ports are laid out on the back. IMHO it makes more sense to put the paired ports next to each other horizontally instead of the up/down/all around arrangement they used.
Real World Speeds in reality is the sum of all components of a system, not just one or two features/components. With very few exceptions, the nMP out performs all others.
As to the HD Bay you list here and the 2 you list on another thread, be aware that these are TB1 not TB2. On the other thread you mention RAID5 which Apple does not support. It takes at least 3 drives to implement RAID5 and is mostly only implemented with hardware chips in the external bay box. That's why the CalDigit 3 bay does not do RAID5 as it depends on Disk Utility for software based RAID. No reason that Apple couldn't update DU to support RAID5 as software, but it does use compute cycles.
LaCie now has a 2 Bay portable TB2 Little Big Disk product out that looks nice, no experience with it though.
Also if you are planning on swapping drives often, I would recommend bays that use caddy/trays that do not require you to disassemble the unit to install/remove drives. Hot swap is also very nice and the ability to power off any drives not in use.
Hope this helps, Greg