The difference between a "Framework Plugin" and a normal "PHP include" is that you don't need to remove head tags, body tags, etc... from the included file. All you do is create a full page the way you normally would - then the framework includes it properly into the master page. It puts the head within the Head - and the Body at the location it needs to be.
I've yet to see how this is any different than a regular server side include.
For instance, I design all my sites with "includes". I do the same as you noted and take the header into it's own file, same with footer and any nav bars (which also usually contain dynamic menu links). Then my basic DW template links to all these files via server side includes. If I need change or add a menu link, it's only needed to be done in one file. The whole site is then up to date.
I picked up this new extension and so far see if as introducing a "conditional include". But that's all so far. No groundbreaking changes if you know how to code in php.
So maybe I am missing something, or need to give the extension some more testing.
What I would like to see is that ability to edit the includes/plugins after they are created. In context. Meaning within a page so that the CSS and other relational elements are present when you make changes. Otherwise we are back to having to reassemble the template page as it was before you separated the various includes files.
DW CS5 was supposed to do this so you could edit a Wordpress Theme in an assembled state. I've yet to have the time to search this out in DW as I save my master templates and can make adjustments in that environment then cut the portion changed and update the include.
Conditional Includes... Cool. I'll figure out something to use this for