You question about the texture on the underside of the screw heads - it's to give them just a little grip so they don't back out on their own.
Something I do, well two things when assembling PC's, is / are: 1) Keep telling myself "it's a computer, not a tank, don't have to overtighten everything", and 2) I use a very small screwdriver with a skinny handle, so I can't get all that much grip and torque on it to start with. Keeps me from overtightening things if #1 fails to work.
Also - you shouldn't of course encounter any cracking / breaking type noises, but I will say that some setups do squeak and make noises when going together. Seems to be "normal".
Also, in the future, you may want to lay the motherboard on a towel or something on a table in a well lit area. Then install the CPU, RAM, etc. Then put it into the case and screw the motherboard down. You can more easily see how things are fitting, and don't take a chance on flexing the motherboard itself pushing things into it later when it's just held up by some screws.
One other thing - on getting answers to your questions, much of it has to do with how you ask them. You give lots of info, provide pictures, ask specific things, and are clearly happy to get the help. It makes it easy for people to give you help and want to do it. There's a lot of other newbies that could take an example from that. So - good job on your side too I guess.