As long as it creates 3d objects and at least exports to a workable format it should be fine. Applying textures and handling hardpoints might be out of the question, depending on what the program is capable of. You would undoubtedly need a way to convert it to .mod, which means at some point you would have to use 3ds Max or Milkshape. Depending on the format that it supports, you also might need a file converter that could resave the file in another format for 3ds/Ms3d to read.
The biggest issue with these varying programs is that you still need one of the above two to get a ship into .mod. Beyond that, it's just a matter of learning how to build/texture the model.