Tim,
A couple of thoughts. If you give the homeworld hub a space yard ability, I think that means you won't get the regular shipyard in the initial build, and I know it means that you cannot build the shipyard later, as there is a limit of one space yard per planet.
Also, one of the things I liked in another mod was the idea of something like the Homeworld hubs, only perhaps "suburbs" that had the same values but not the one-time abilities, and cost a bit less. Then, you could slowly convert your homeworld into a more "urban" place by replacing the resource colonies with "urban" ones.
Also, I think the HH needs to improve planet conditions. The slowly growing races, like the Minbari and Centauri, are really screwed compared to the fast-growing races like the Narn because their populations don't grow at all on an unpleasant planet (and the homeworlds are all unpleasant at the start, I believe). Having the HH make the planet more pleasant over time makes these races much more competitive later in the game, as their homeworlds start to grow back in population and they get the production and generation bonuses.
Re the palace for the Trading port: are you sure the AI_Construction_Facilties is calling for it to be built first (i.e. that you are using my Version)? Have you tried moving the racial AI_C_F files to a temprary folder and putting the AI_C_F I uploaded into the AI folder as Generic_AI_Contruction_Facilities.txt, so that all races use it?
Try that, and allow 50 or so turns to go by so that the AI players have a chance to start a colony in a new system, and see if the AI is building a Trading Port.
I cannot see how this would work for me and not for you!
If all else fails, you can just make all races "Natural Merchants" and eliminate the Space Port ability from the game entirely.