Just so I can plan ahead, what missions give me planet transformers (like gaia seeds), or just give me planets (like aphotic planets)? What ranks are they unlocked at, and what are the missions that start the chain?

You can look all of these up in the wiki?

Go to the wiki and click on Planets, scroll down and you'll see Player Made, which is exactly the ones you are talking about. It will say how to get them, give a link to the missions (which can then be followed back to find the start of the chain) and also the size and richness of resources for each and how many are available.

Never thought to look under planets.
looks like to only ones I can get right now are crystal/irradiated. Need another 30-75 ranks for the others.