Um, no I don't quite understand that. Once you have installed the prop tubes in a model it would be very unusual indeed to have to remove them. I have only found it necessary to do so once in 50 years of modelling! It is certainly not normal modelling practice to provide for prop tube removal. If there is an imbalance problem then replacing the bearing inserts would be the usual solution but on a scale model this would be very rare too.
Most commercial scale props will be sufficiently balanced not to result in significant oval wear in a scale boat prop tube bearing.
In the very unlikely event of having to extract the tube itself then the paint would be on the outer end so would not impede the withdrawal of the tube.
To be honest, I think you are worrying too much!
Colin