I see the problem.
I guess this just isn't possible without coding. It would still be cool to implement this. Because each craft has a unique name, doesn't it? INTERCEPTOR-1, INTERCEPTOR-2 and so on, unless you re-named them, but the name does need to be unique, doesn't it? So it would theoretically be possible to add custom "mod-construction" jobs, like "install alien alloy plating" which then asks you to select the craft that is supposed to be modified.