I've added those 2 mods as incompatible now in 2.1.3, makes sense that if my mod and those mods are both trying to replace the spaceship entities that it would conflict.
Can you just ignore anything altered by other mods and only convert those that have been left alone? It would still be fun to scrap all of the bits and bobs left scattered around.
If not, could you make (default off) options to be able to mine the main ship/ship assemblers/etc? That would avoid conflicts with other mods completely.