Hmmmm - interesting observations!
2)Some new automatic designs allow me to build ships that I normally
would not be able to build due to limits of miniaturization...
3) An AI colony ship is stuck to a corner of the map.
5)Personally, I would prefer that the AI did not trade its unique techs
(so easily)...
About;
2- I really do believe the Ship_Design_Focus option will eventually become centralistic to any Macman enhancing feature in this game. All or any upgrades to this essential tool should be given high priority by SD. It's a rather tough intuitive undertaking to say the least - cuz it would involve player's choice and/or pre-defined deterministic needs as it also relates to;
a) What tech level has been reached in numerous areas,

Which preferences could be made common or relative to emergency design switching,
c) Restrictions applied (or not, btw) to certain Hull-types or categories when & then upon selection by the player.
d) And, plenty more possibilities.
About;
3- This has been known to me for a long time and i never cared much about asking why here. I suspect this 'idled_ship' is a code loop indirect tapper of map conditions devised by the coders as either, a bug trap, or a calculated risk toward monitoring specific gameplay issues. But, that's my guess only. It may prove to be just a simple glitch. All i know is that the thingy isn't selectable, my ships could simply go on that tile and share the location with an indirect 'invisible' ship, etc. It's there. Bof - for some unclear reasons. Doesn't interfere with my games though.
About;
5-Nope, it is sooooooo funny & weird that i find the extra-element of back&forth distribution of almost exclusive stuff a welcomed challenging situation. There are, in fact, some untradable items... but, in these cases it actually makes
much more sense.
Sooooo, all things being said - i figure the complexity introduced by the multiple trees is the core feature which may keep us all busy for a loooooong time. And with the editors we can always inspect values to satisfy our curiosity. Kudos to SD for daring that much, btw.