You can still use the silicone... BUT, you MUST let it cure before you fully clamp the two pieces together.
Best to lay a bead down, then set the pespex top on to create a flat gasket shape. Let it cure 24 hours if that's what the tube directions tell you is the cure time of the silicone.
THEN and only then... torque down your screws/bolts to clamp the two pieces together. This will squash your new gasket and seal the pieces.
Hope that helps.