The "best" designs for population transports (and most other ship types) changes depending on which techs you research and in what order. Also, because research is generally slower than in the standard game, you can't just fill up a few huge planets with research centers and then zoom to the end of a few tech areas and then just build the best designs. So, you need to decide how much to invest at what tech levels.
Fyron and Oleg answered most of your questions, but:
Ya, 2.3 added a second duplicate resupply depot, for the AI to know what to build, but I forgot to remove the first one. So there's no difference.
"Never" means "practically never under current conditions" (over 100 years).
System-wide warning is just a built in convenience factor. Ignore it if you know you want what you're building - it is just an unsophisticated warning.
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In the tech tree, there is a "Colony Ship (Rock)" but no corresponding tech for ice or gas. Is this unique to rock? Other things on the tech tree make me think the tree is not quite completed.
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That is an experiment for the AI that doesn't actually appear during play in current Versions. I probably should have hacked it out of the files to avoid confusion.
Colonial Community is a cheap low-tech, relatively low-cost, multi-function facility that can upgrade from Colonial Settlement.
Agrarian Colonization is good for worlds with high organic values, and/or when you want to concentrate on organics production. I think it also has slightly higher happiness mods in some cases than equivalent industrial urban facilities.
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"Colonial Development" and "Large Support Facilities". Are these really just for the AI, or should I be researching them anyway?
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It's up to you, but you probably want to research them at least a bit. By waiting to research them, it does allow you to limit what your colonies will upgrade to when you order a facility upgrade of those types.
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Thats about all for now, except to say I muchly approve the many tech items that require more than one prerequisite. Not so linear, more intertwined, and much more fun!
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Thanks!
PvK