Hmm, Im wondering if I misunderstand what you are saying. What I have written seems to make sence to me. I can only think that you misunderstand the meaning of the CR, neglecting the combustion chamber.
So, shorter conrods than stock = Same compression ratio?
Lets work it out for a G40.
so: (((3.14xbore squared)/4)x stroke) + combustion chamber volume
CR: ---------------------------------------------------------
Combustion chamber
I have no idea on the size of the combustion chamber for the G40, it can be derived from the formula but I cant be arsed.
For the purpose of this I will just say it is 50000mm3, bore 75.00 mm and stroke 72.00 mm
Bang the numbers in and we end up with somthing that starts to look a bit like this...
(4416 x 72) + 50000
CR: ----------------------
50000
CR: 7.3585 (:1)
So now lets say we have shorter con rods. Same swept volume (because the stroke remains the same) but the piston does notrise as high at TDC, and at BDC it sits lower. Lets say we use con rods that are 2mm shorter. So now we have more volume in our combustion chamber, 2mm multiplied by the cross sectional area of the bore is 8832 mm3
So back into the same eqn
(4416 x 72) + (50000 + 8832)
CR: ---------------------------
(50000 +8832)
CR: 6.404 (:1)
Which is lower.