When you tell it to load a mod using the -mod command, it will load the ships.tbl and stuff from that mod only. In the case of the mod not having a ships.tbl, it'll use the retail ships.tbl.
What you are trying to do will probably not work. Even if you were to take all the FS1-specific stuff from the Port's tables, turn it into a shp.tbm file and load that... it would exceed the 130 ships limit, and the program would yell at you through error messages.
Same thing with downloaded ships, you'd have to add them in through shp.tbm files.
I don't know exactly what you are doing, but I get the feeling it's something rather grandiose. The fact of the matter is that FS2 will only accept 130 different ship classes in one mod. Anything beyond that it will simply ignore.
You might be able to get away with it if you used an Inferno build, which allows 300 ships rather than 130, but I'm not sure.