I assure you that LogiCrap stuff works just fine without their so called "pots." [Those pots win the prize as the crappiest pots I have EVER seen!] I have been running a hybrid CH ForceFX / Logitech FF 3D whatever in a similar way the Pro Pedals are done. It works perfectly. I certainly would not be afraid to use the PCBs. After all, no moving parts, etc. If it works the first time, it should work every time. What's crappy about Logitech other than the pots, is their gimbals, switch housings, springs, etc. And that stuff is totally crappy!
Here is that project:
FrankenForce project One reason you might want to look at something a little better though (eg. Saitek Evo) is to get better programming software. Logitech software is pretty minimal. Saitek appears a good bit better. I use Logitech stuff because I can pick up a Logitech stick for less than $10.
As for you question about rotaries vs axes. A controller only has two types of interface controls: buttons and axes. [At least I don't know of any other kind] Therefore, my educated guess as to what people mean by that is a rotary would be an axis that is controlled by a knob of some sort (something you have to turn) whereas an "axis" is just the basic analog pot which could be a "slider", "rotary", "lever", etc.
Can you put a trim wheel on ANY axis? Absolutely. A pot is a pot. Some pots are rotaries (twist them) and some are sliders (you guessed it: you slide it). Other than that, it's just a device that produces a variable resistance to the circuit.
As for adding axes. If you can figure out a way, I want to be the first to find out. I think I can safely say NO to that question. I have never seen a joystick with more that four axes. Of course, the CH Throttle Quadrant has six axes but you will pay $150 for one of those. As you pointed out, people make USB controller boards used by pit makers that support various configurations. That is probably the best bet if you really want to go beyond four axes.
Hope that gives you more decision power.
-hb