It is possible to build a full site with Hype - if you’re building a “brochure” site. My major concern with Hype for a full site is how it handles SEO. By default, I’m thinking that a CMS (like WordPress or Drupal) would probably get better SEO results, while Hype would likely get better design results. WordPress and Drupal are often used for more newsy looking websites.
I’ve seen Hype sites that use separate projects for individual pages… which could be somewhat better for SEO, but is an awkward transition.
Hype has layers and elements can be pinned and be flexible. With Hype Pro, there are persistent symbols. I’m not entirely sure if Hype will meet all of your requirements, as I’m not entirely sure what they are, but it does seem that you’re probably in the right spot.
An element on top of a background can work like a button to change the background. I think the concern is not so much Hype, but the size of the project. Lots of large images can slow things down.
Getting an element to stick to a certain place in the picture might be tricky. Document scaling is an issue right now, as multiple elements don’t scale as easily as they would in Flash, but there are interesting thread about this on this forum…