I'm reading this and getting very confused.
Brrt (and SuburbanWorrier, to some extent)
I really don't see the need for such precision.
I'm assuming that you will have no control over what size/resolution/density - Retina displays anyone? - the screen will have when the document is reviewed so it will have to be resized in a way that you have little-to-no control over how it looks anyway. So why bother trying to be so precise when you have no way of knowing how the document will be seen?
Isn't it better to concentrate on getting it looking good as opposed to getting it looking precise? Even bitmaps are scaled on different screens so their pixels won't be guaranteed to be on pixel boundaries - and therefore may not be drawn "properly" - so you can't assume anything.
SuburbanWorrier (and Brrt, to some extent)
I'm not really sure what you want.
For web prototyping I think you might be better off using something like invision
http://www.invisionapp.com/ (many alternatives are available but I just happen to know that this one is free for messing around with).
If you're prototyping in Scribus (or whatever else), and then have to translate that design to the web, you're going to have to re-design anyway. So why not use a prototyping tool that allows you to use the prototype in the finished design?
You say it makes no sense to work on print based designs but that's exactly what you're doing when working in Scribus. You have to translate the text/image frames etc. into <div>s and whatnot anyway so why not use something where you don't have to do the translation? And then there's the whole responsive design thing to take into account. It really makes no sense - to me, at least - to be designing a static page in Scribus for later use on the web where everything is different.
It might be good for quick mock-ups, but if you're being so precise in a mock-up then you may be putting too much work into the wrong things. Work on the overall "feel" in the mock-up then be precise in your CSS later.
BothWithout knowing exactly what you're each trying to do I can't really give more specific advice but I think you could be "overthinking" this a bit.
Scribus is a (printed) page design tool. It's not a free replacement for InDesign or Quark (or anything else). It's its own thing and it does what it does very well. It would be nice if it could do more but I think you're asking for a little too much from it.
Apologies if I sound overly argumentative - that's really not my intention - but I'm frankly baffled by the requirements given.