Anywhere there are molded parts, you will have a filet that will interfere with the mating part. There is a radius in the mold purposefully. If the inside edge was square it will not allow the mold to release the part well.
Try squaring the inside edge, where the door sits, with a sanding block. If it still needs more, sand down the entire surface where the doors nests. It doesn't take long to sand it down to the depth you need for your door to sit flush. Keep the surface flat and square by using the sanding block.
This same issue exists with wing tips and empennage tips. Sanding block with a sharp edge will clean the mating joint up and allow a better fit.
Smart People do Stupid things all the time. I know, I've seen me do'em.
RV6 - Builder/Flying
Fiat G.46 -(restoration in progress, if I have enough life left in me)
RV1 - Proud Pilot.