Valve Clearance on Larger Camshaft and Flat Top Pistons

To your questions, assuming you have had to cut the reliefs deeper to get clearance. Would you need to have a piston with a pop up to regain compression? No, go thinner head gasket. Cometic makes an .029 gasket with other thicker options before you get to .050. That being said a pop up can help with quench.