For whatever reason anything a champion starts with is "theirs" and cannot be sold. Perhaps this is to avoid "rebating" their price by stripping them to their skivvies and selling everything off. Perhaps those items hold a great deal of sentimental value.

If you don't mind me adding to your list:

4. The inability for custom sovereigns to pick up the "Organized" trait. This is one of the few traits you can build an entire strategy around, and I have to choose between Markinn or Kulan in order to gain access to it?

1. Actually, you can click on one of the things that the tech gives you, opening it in the Hiergamamnon, and then navigate from there to the tech to look at other things. An Info button might still be nice, though.