Away from the computer, I've now had a good think about this matter, and I reckon I've sussed out basically what's meant to happen. Possibly, this may have already been blindingly obvious to you and others, DM, but not to me. This still leaves a few unknowns, though. Feel free to pick holes in this.
Here's what I think happens. Consider the labeled four pins of the CPU fan header. In the BIOS, when you put the Fan Mode to Voltage, the CPU controls the speed of the CPU fan by varying the voltage on Pin 2 of the header, and the CPU will do this according to its core temperature. Conversely, if you put the Fan Mode to PWM, the voltage on Pin 2 will revert to a fixed value of around +12v and instead a PWM signal will function on Pin 4, controlling the speed instead by that method. Again, that PWM signal will be actioned by the CPU and will be a function of the CPU's core temperature. If you completely disable Smart Fan Control, then PWM is curtailed, as is also Voltage control, and the voltage on Pin 2 will revert to around +12v, making the fan run at full speed all the time.
I suspect that the Sys 2 Fan header works in much the same way. That is, it uses Voltage control on its Pin 2 in order to determine its fan's speed. However, Sys 2 fan header doesn't have any PWM control. And if you disable Smart Fan Control, I reckon the voltage on Pin 2 will again revert to a fixed value of around +12v, making the fan run at maximum speed.
lf my conclusions are correct, it should mean that, if I disable Smart Fan Control and then connect the CPU PWM fan via a Fanmate2 (no, not a PWM Mate, a Fanmate), the Fanmate should allow me to manually control the speed of the CPU fan. There's of course a physical mismatch with the connectors (3-pin to 4-pin) but this can easily be overcome by just snipping away one outer edge of the Fanmate's 3-pin connector. Once the speed is set manually in this way, of course, it won't then vary with temperature but if I'm confident about the likely heat increase and I gauge the required fan speed correctly, I should be able to set the fan's speed somewhere between its minimum and maximum and adequate cooling will result, consistent with achieving minimum noise. This method will avoid having to later install the Easytune utility just to be able to set the speed.
The Sys 2 fan should similarly be manually controllable by a Fanmate but, without experimenting, I'm unsure as to whether disabling Smart Fan Control will also disable the Voltage control of the Sys 2 fan. I suspect that, with Smart Fan Control enabled, the speed of the Sys 2 fan will be determined by the CPU and its sensing of the air temperature in the case. It could well be that, in my situation, the case temperature has not, as yet, been high enough to warrant the Sys 2 fan, ie. the inlet fan, being on. So, maybe that's why the voltage on its Pin 2 is only around +5.4v. (Earlier, DM, you hinted that this might have been the situation). This would be a reasonable way of automatically operating the inlet fan but, frankly, wouldn't be my first choice. As with the CPU fan, I'd rather have complete manual control of it, making it run at a fixed low speed all the time. Again, the manual control solution would seem to be to operate the Sys 2 fan via a Fanmate.