I find with my dress boots that they are too tall in the foot, so I need insoles to keep them on anyways. They are semi-custom Petrie 3000s.
Generally, custom boots are custom in style, sizing, etc and they don't really do insoles as far as I know?? Your best option is probably just to go for semi-custom and add your own insoles.
Plus really, how much walking are you doing in your boots? In order to keep them the correct shape and not wear them out quickly you really should be putting them on right before you ride, taking them off right after and never exposing them to a lot of water.