The galactic projects you are noticing are being occurring as intended. Several races get early galactic projects. For example, the Arceans get the Stellar Forge that only their unique "tech" "A Glorious History" will allow. They get that tech at the beginning of the game and thus can begin building it immediately. The Terrans get the Innovation Complex under similar circumstances. The Thalan's entire early game infrastructure is based on a series of galactic projects only they can build.

The generous system you describe is most likely just a lucky happenstance but the number of habitable planets depends on the game play settings you establish during game set up. If you have abundant habitable planets, then the odds of a system like you describe greatly increase.

The green thumb type racial abilities increase the number of tiles available to the race possessing the ability. Those tiles appear upon colonization by that race over and above the number otherwise available to races without the ability.

When you conquer a planet the population becomes consistent with those of your own race depending on its technology and abilities. If you possess knoweldge of alien techs and are abel to keep some of it upon conquest of the planet, then th alien tech may play into determining the population. For example, the Torians have a unique agriculture "building" that you might be able to use if you conquer one of their planets and possess the tech to build that structure (and manage not to destroy it during the invasion).

I hope I answered your questions.

You should get the extra tiles when you conquer a planet just like when you colonize it. I don't know about getting back planet quality diminished by invasion-I don't think I've ever used those tactics.

There are technologies, like the Arcean Weather Control Zenith, that will increase planet quality. That should be in addition to the bonus you would get from the race attribute.

In Twilight, if you do not have possession of a racial tech (not all techs), then it will disappear upon invasion of an alien planet that has the applications from those techs constructed on it. For example, if you successfully invade an Iconian planet with precursor libraries and you don't have the tech to enable you to build that application, then all of those buildings will be eliminated. On the other hand, if that same Iconian planet has industrial sectors on it and you only have the advanced factory tech, then you should keep the industrial sectors.

Regarding moral alignment - research Xeno Ethics and you can officially pick an alignment.

Until you research this, you can modify your ethical leaning by your choices on the moral questions. You'll notice that if you get a bunch of these before researching XE, it will affect the price to select each ethical orientation.