Small ridges on the canopy probably won't "lock" the part up in the mold, since there is some flexibility to thin layups. If the "plug" came out of the mold, the parts should. Using a blast of air, especially if you only have a slight draft in your mold, helps to pop parts out of the mold. Your plan to build the internal structure, and form the molded parts over it should work. Give it a try, and see if it gives you the results you desire. Keep in mind that most glass fuselages are joined as a unit, and then the internal structure placed inside. The typical model only requires a minimum of reinforcing parts: a firewall, wing hold down plates, stab doublers, maybe a rudder post, and servo rails.