Choose a domain and stick with it, then build pages out from there. Redirect the non-www to the www (if this is what you choose to go with) and forget about the rest... redirect site-wide.

Admittedly I'm simplifying it for two reasons: 1.) I'm not quite sure I get it, this is rather confusing and 2.) it is that simple.

You want a domain and then you want pages and subdirectories targeting your keywords. That's it that's all. I would not build links for the non-www if you are going to redirect for the www. Build links for the domain you settle on.

I'm not sure I'm helping but hope so!

Question 1:  No! Why not just create the internal page and have it target the specific keyword? Your homepage is your brand, not a product/service page. Those are internal. They will rank for whatever you are targeting (if your SEO campaign is strong). Why are you worried about what your homepage ranks for?

Short answer: No. Make internal product/service pages targeting specific keywords and do not redirect your home page.

Question 2: Huh? Those two examples seemed exactly the same to me. Are you asking why some pages will show a sub directory and some pages will show the html page in the URL? If so, it's all in your structure. It doesn't really matter which way you wanna do it but having multiple directories may give you the opportunity to attach keyword targets such as "example.com/services/stuff-i-do.html" as opposed to "example.com/stuff-i-do.html"

The former example will bring the word "services" into your string.. IF you are trying to get your page to just read "example.com/services" then just create that directory and drop an index page in.

Hope this answers your questions or at least comes close.

No truth to that whatsoever. That's weird paranoia.

If there was some sort of problem WITH the content, maybe. But there would be no penalty for all new content added.

I've done total site overhauls plenty of times and they get indexed quick with no penalties.. (although I will say the speed of this seems to be in flux, but I digress.)

Don't let the client worry about this. Think about any website that initially launches: why would Google penalize that?

Hope this helps. Paranoia is often the toughest challenge when it comes to dealing with clients/site owners.