I think you're think ahead of what's possible.
Initially Alternate Layouts are aimed at print or Web uses where you want two or more different versions of a layout. In the current version 1 of this implementation, you can have differing page size and orientations. You can link text and graphics between alternate layouts. You can do style mapping between layouts. You can use the Smart Text Reflow feature to accomodate adding extra pages.
But there is no way to have each alternate look toward another layer. So your use case isn't possible (as far as I know, perhaps it could be scripted).
Also, each alternate layout uses the same swatches and ruler measurements so it wouldn't be possible to share both a print layout and a web layout in the same document. Another use case which is not dealt with yet.
Maybe in the next version of InDesign?
In Belgium, most publications are multilingual. In the past we also had some trouble to convince Quark that this was a main issue in Europe to combine multiple hyphenation methods in one document (we did some betatesting on several versions). This is still not solved entirely, because the dictionaries are not quite reliable. And to get all text straight, we need to implement dozens of specific paragraph styles... and a lot of manual checking.
The control by layers, or simply spoken: to be able to split the document into enclosed entities to control text and objects completely independant from other layers, would be a great option. As well for the different layouts, which need also adaptation to their target medium (colours, typefaces, line thicknesses, etc).
And when the hype of tablets will be over and settled, we will probably urge for a more modular way of making layouts: controlling text and image input apart from any layout structure.
I cannot believe that this is a difficult aim, for this has been implemented in the nineties with several other advanced typesetting systems, not really commercial on a broad scale, but focussed on a professional way of graphic design, also to split up human tasks in a production process.
Anyway, I will be looking for some plug-ins which could solve my biggest concerns, while Adobe hopefully will come with a more open architecture in Indesign.