It looks like the top plate has the shell thickness all below it, while the bottom plates have the shell thickness all above it.

As long as these offsets are correctly defined, and the combined thickness of the two shells equals the geometric gap between the surfaces, the contact gap/penetration should compute as closed to within a very small error if the shell thickness effect is turned on for the contact between the lower plates and the upper plate.

You will also need contact between the bolt heads and the upper plate.

You will need bonded contact between the bolt shaft and the lower plates, however, you should divide the face of the bolt shaft so the lower portion is used in the bonded contact while the upper half of the bolt shaft could be used for a bolt preload.