When you create a Flash swf file it has one stage size, and that stage size is whatever you make it.
Most people design a Flash site to fit within the browser window size and not have one that requires scrolling. In that scenario, if scrolling were necessary, the scrolling would be built into the swf and the browser scrolling would remain unaffected.
For a site that varies in height from page to page, it would be more likely to not create a Flash site, and instead create individual pages for each section.
So in a way you have kind of answered your own question. If you want to use Flash for the design and you want to have the different sections only scroll as much as necessary using the browser scroller, the easiest way to accomplish that is to have each page as a separate html page containing a separate swf file.