Puke, great minds think alike. SJ and I were having a conversation about this very a little while ago. Your idea is almost exactly what we came up with. I was thinking you wouldn't need to have the freighters be more expensive though. Say the freigthers are cheap enough to build at a colony in one turn. Then you build a stream of them and send them back to your homeworld to be scrapped. There is nothing to stop you from building them at your homeworld too, but if you do the percentages right, say 120% scrap return, then you aren't exactly going to get rich by just building and scrapping merchant ships at the homeworld. You'd need lots of colonies sending streams of them home to expand your empire. Plus if you are building merchants at home you aren't building war ships or colony ships. And that's a bad thing.
For it to work though you'd need to remove the orbital yards from the mod. Otherwise you could get around having to travel by building a bunch of space stations to crank out merchants.