I do not know of any one package that does all the things you ask. Almost everything you mention can be accomplished with a combination of packages.
While BookDesigner (I assume that you have the BD4 release and have applied all updates through the March 15, 2007 update) can convert directly to IMP and LRF, the results are sometimes suboptimal and a bit of reformat is required.
No package that I have ever found can strip out the page headers and page numbers and page footers of a PDF in converstion. For that I have used Adobe Acrobat Professional and cropped the pages to exclude these areas and then extracted the remaining text. On most cases this works. On one project the page headers still showed up in the resultant extraction. I use ABC Amber PDF Converter.
I tend to extract the text and then do my editing in Word. I use Stingo's Word Macro from the MobileRead Wiki Conversion page to remove the end of line page breaks. This becomes a bit dicey when there is only an indent to signal a new paragraph and certain preactons must be performed to replace the indent with another paragraph mark. Once the paragraphs are set as units rather than a collection of lines the reflowing will work fine.
As I understand the program, BD5 allows for the setting of margins and can produce a TOC. I have not pushed at the TOC function much but the default seems to work.
It seems rather strange to want to set the margins and have reflow while wanting to keep the paragraph formatting intact. The line breaks and paragraphs per page cannot stand or be the same while changing the size. Also, the PDF that was used as a source is most likely either letter or A4 sized. The only answer there would be to load the PDF directly on the Reader which would produce a letter size too small to read.
DB5 can produce files in both IMP and LRF from the same source file. I think everything you need for formatting the output is in BD5, you may just have to dig a little more at the documentation.
As for what Sony uses, they invented and control the format so their tool is an internally generated one.
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