GK: Like a few others said, the old-style trade routes live on in City Connections, giving you a gold bonus for using roads to link your cities together. You can build as many caravans and cargo ships as you'd like, but you can only have up to 10 trade routes active at any given time (8 from technologies, 2 from wonders, the list is on the first page of the thread). I've heard from several places that roads can exchange the range of your land trade routes, but I can't find anything in the Civilopedia that confirms that. It might be one of those things that we just have to discover through experimentation. I can say that Combustion "extends the range of land trade routes," but again, I don't have any specific information beyond the tooltip in the tech tree.
Tinker: I haven't run into Portugal yet, but from pre-release interviews, the devs said that Feitorias will remain in place, funneling a copy of the luxury resource to Portugal as if the CS had never been taken. No word on if the new owner still gets a copy of the resource, or if they have to destroy the Feitoria and declare war on Portugal to get whatever's beneath it.