The database schema does allow several products to have the same SKU. This may well be a design decision to allow the very thing you're proposing. In my very limited testing, it seems like there's nothing to stop you having several products sharing the one SKU.
Note that this version (Stock & Price CSV Updater 2) is designed to handle your case. The original version won't handle it properly, as it doesn't differentiate between products that have the same SKU.
As for the package stuff, I've yet to investigate this. I know Ubercart has a "product kit" feature that provides this kind of functionality, but I don't know how stock levels of a kit's components are handled.