Hello!
I agree that it would be very nice if the fuselage seam would be designed with filling and sanding in mind. Covering it with varoius bumps and the likes helps to hide it. The same could be said about the wing seams, although those are easier.
I'm not sure what Don meant about the flanges - Don, could you write more about it?
As for the undercariages - this was always hard. A strut that goes into a hole in the fuselage is usually not how it is done in a real aircraft with retractable gear, and replicating the complicated joint at the base of the strut usually isn't done in smaller scales, so we have to do our engineering here anyhow.
Good luck with your modelling projects and have a nice day
Paweł