Yes it is irrelevant to the force in the bolts, but not to the changes of length and strain and hence distance measurements. I assume that was why you (rightly) asked the question how were the distance measurements made. The OP states "I want to calculate the 'deflection' at this point on the surface".
But the deflection from what?
A surface plate the whole assembly is standing on?
The contact surface between the sole plate and the block?
I agree that between any two sections or marks on the unstressed block, the compression will only depend upon the applied force, not the method by which it is applied.
However something must change position in the system, so if measurement is made from an external reference, this must be taken into account.
A question for varatharajan.
It is possible to have stress without strain or strain without stress.
Can you say how?