I can't believe you have not watched all of the videos...every minute! Yeah, the videos are long, winding, and I am such a dynamic character. ;> Essentially just twitch streams, I wanted people to get a feel for how it is going, that there is something there, and most of those are August/September. I need to do another as by your questions the interface has changed to where what you are asking about is covered. For the specific questions:
1)You don't get a tool tip, instead there is an info box in the lower right (or left) corner which gives some info for any location your mouse is over, more than I think EDEE did. there is also the status bar and a lower section which provide info on the current active unit.
2) The EDEE side window was admittedly clumsy, so for this version there is a right click menu, and it can be used to do things like command a unit or open production. The right click menu is an optional thing as you have most commands/actions available without a right click. However, the nature of clicking as a whole is varied now. My testers really worked on me to facilitate several different styles. There are four ways to set what your clicks mean. I think some of that is explained in this update blog.
3) The handicaps. These percentages are masked as they are actually weights that work in formulas that are not that straight forward. My recommendation is to use one and see what the impact is on building a simple army or fighter at 100 to get the impact. I frankly cannot off the top of my head tell you the percentage impact. In EDCE there is this concept of an "account" (completely offline and internal to the game), and you can set up an account just for experimentation and such, and mess with the game not worrying about impacting the play stats for your other account(s).
And man we are getting closer. I just played the game on Steam the first time yesterday. Hard to believe but release is coming. The pre-sales period is going to end very soon. And I am still having fun.