I don't foresee a matching set of aftermarket wheels/tires causing the issues you're reading about.
Changing the diameter from stock, on all four corners, should not present any issue. If you go up to say 31" tires all around and ever need to put on a ~28" spare, you could possibly run into...
Side wall height is NOT 65mm, it's 65% of the width. The suspension does not change height in any way between FX4 or non-FX4. Monotube rear shocks don't provide lift. As far as we know, there's zero difference in the front suspension either. If Ford lifted the FX4 model, we'd know about it...
Where are you getting 8.6" from FX4? The 8.6" is ONLY when equipped with the 235/65R17 (which just happen to be 0.5" taller than the standard tire size). Thus an FX4, with standard 225/65R17 Pirellis will have the same ground clearance as FWD Hybird, 8.3". The only way to increase ground...