Here is the full picture without top part, Sorry I didn't include it earlier. The five bolts will seal the joint.
To your last question, with pretension the whole gasket (Rubber and metal carrier) will be compressed. If I stop the analysis when bottom part is flush with carrier, That won't give me results I am looking for. Because, the carrier also acts as gasket and gets compressed and helps seal the joint.
I am trying what you suggested but also help me with analysis with pretension.